Release v0.4.1

Cache AUR package providers #23

.gitignore

@@ -4,3 +4,4 @@ build/
 *.egg-info/
 
 venv/
+dist/

README.md

@@ -1,5 +1,18 @@
 # Decman
 
+> 🎉 Early support for Flatpaks was just added! 🎉
+> By default flatpak management is disabled. Support is in early stages so expect bugs.
+
+> ```py
+> import decman
+> import decman.config
+> decman.config.enable_flatpak = True
+> # You can add system wide packages as well as user packages
+> decman.flatpak_packages += ["org.signal.Signal"]
+> decman.flatpak_user_packages["user"] = decman.flatpak_user_packages.get("user", [])
+> decman.flatpak_user_packages["user"].append("dev.zed.Zed")
+> ```
+
 Decman is a declarative package & configuration manager for Arch Linux. It allows you to manage installed packages, your dotfiles, enabled systemd units, and run commands automatically. Your system is configured using python so your configuration can be very adaptive.
 
 If you want, you can also use decman with other configuration languages. See the [example with TOML later in this README](#decman-with-other-configuration-languages).
@@ -80,6 +93,8 @@ Then import your module in your main source file.
 import decman
 from syncthing import Syncthing
 
+# NOTE! Removing a enabled module from decman.module means that on_disable will not run.
+# Instead disable the module.
 decman.modules += [Syncthing()]
 ```
 
@@ -109,17 +124,22 @@ decman --help
 Clone the decman PKGBUILD:
 
 ```sh
-git clone https://github.com/kiviktnm/decman-pkgbuild.git
+git clone https://aur.archlinux.org/decman.git
 ```
 
 Review the PKGBUILD and install it.
 
 ```sh
-cd decman-pkgbuild
+cd decman
 makepkg -si
 ```
 
-So far I have not created an AUR package for decman, because I'm not sure if other people would find decman useful.
+Remember to add decman to its own configuration.
+
+```py
+import decman
+decman.aur_packages += ["decman"]
+```
 
 ## What decman manages?
 
@@ -127,6 +147,8 @@ So far I have not created an AUR package for decman, because I'm not sure if oth
 
 Decman can be used to install pacman packages. Decman will install all packages defined in the source and **remove** all explicitly installed packages not defined in the source. You don't need to list dependencies as those will be handeled by pacman. You can set packages to be ignored by decman, so that it won't install them nor remove them.
 
+Please keep in mind that decman doesn't play well with package groups, since all packages part of that group will be installed explicitly. After the initial run decman will now try to remove those packages since it only knows that the group itself should be explicitly installed. Instead of package groups, use meta packages.
+
 ```py
 # Include both foreign and pacman packages here.
 decman.ignored_packages += ["yay", "opendoas"]
@@ -143,12 +165,13 @@ Decman can install AUR packages as well as user defined packages. Foreign packag
 Here is an example of a user package. Managing user packages is somewhat cumbersome as you have to declare their versions, dependencies and make dependencies manually. However, you probably won't install many user packages anyway.
 
 ```py
+# Note, decman now has a aur package, I recommend using that instead.
+# Also, this example may be out of date
 decman.user_packages.append(
     decman.UserPackage(
         pkgname="decman-git",
-        # Note, this example may not be up to date
         provides=["decman"],
-        version="0.3.0",
+        version="0.4.1",
         dependencies=["python", "python-requests", "devtools", "pacman", "systemd", "git"],
         make_dependencies=[
             "python-setuptools", "python-build", "python-installer", "python-wheel"
@@ -157,12 +180,15 @@ decman.user_packages.append(
     ))
 ```
 
-Building of foreign packages happens in a chroot. This creates some overhead, but ensures clean builds. By default the chroot is created to `/tmp/decman/build`. I recommend to use a tempfs for the `/tmp/` directory to speed up builds. Also make sure that the tempfs-partition is large enough. I recommend at least 6 GB.
+Building of foreign packages happens in a chroot. This creates some overhead, but ensures clean builds. By default the chroot is created to `/tmp/decman/build`. I recommend to use a tmpfs for the `/tmp/` directory to speed up builds. Also make sure that the tmpfs-partition is large enough. I recommend at least 6 GB.
 
 Build packages are stored in a cache `/var/cache/decman`. By default decman keeps 3 most recent versions of all packages.
 
 ### Systemd units
 
+> [!NOTE]
+> Decman will only enable and disable systemd services. It will not start or stop them.
+
 Decman can enable systemd services, system wide or for a specific user. Decman will enable all units defined in the source, and disable them when they are removed from the source. If a unit is not defined in the source, decman will not touch it.
 
 ### Files
@@ -273,10 +299,11 @@ aur_packages = ["protonvpn"]
 enabled_systemd_units = ["NetworkManager.service"]
 ignored_packages = ["yay"]
 user_packages = [{
+    # Note, decman now has a aur package, I recommend using that instead.
+    # Also, this example may be out of date
     pkgname="decman-git",
-    # Note, this example may not be up to date
     provides=["decman"],
-    version="0.3.0",
+    version="0.4.1",
     dependencies=["python", "python-requests", "devtools", "pacman", "systemd", "git"],
     make_dependencies=[
         "python-setuptools", "python-build", "python-installer", "python-wheel"

example/my_module.py

@@ -1,10 +1,10 @@
 # from import is ok for importing classes and functions
 # just remember to not import variables this way
-from decman import Module, File, Directory, UserPackage, sh, prg
+
+from decman import Directory, File, Module, UserPackage, prg, sh
 
 
 class MyModule(Module):
-
     def __init__(self):
         self.pkgs = ["rust"]
         self.update_rustup = False
@@ -28,6 +28,8 @@ class MyModule(Module):
         # or run a program with arguments.
         prg(["usermod", "--append", "--groups", "mygroup", "kk"])
 
+    # NOTE! Removing a enabled module from decman.module means that on_disable will not run.
+    # Instead disable the module.
     def on_disable(self):
         # You can run commands as any user
         sh("whoami", user="kk")
@@ -58,18 +60,21 @@ class MyModule(Module):
     def files(self) -> dict[str, File]:
         # Variables are substituted in text files automatically.
         return {
-            "/usr/local/bin/say-hello":
+            "/usr/local/bin/say-hello": File(
-            File(content="#!/usr/bin/env bash\necho %msg%", permissions=0o755),
+                content="#!/usr/bin/env bash\necho %msg%", permissions=0o755
+            ),
             # Variables are not substituted in binary files.
-            "/usr/local/share/say-hello/image.png":
+            "/usr/local/share/say-hello/image.png": File(
-            File(source_file="files/i-dont-exist.png", bin_file=True),
+                source_file="files/i-dont-exist.png", bin_file=True
+            ),
         }
 
     def directories(self) -> dict[str, Directory]:
         # Directories are handeled the same way. Variables are substituted in text files.
         return {
-            "/home/kk/.config/mod-app/":
+            "/home/kk/.config/mod-app/": Directory(
-            Directory(source_directory="files/app-config", owner="kk")
+                source_directory="files/app-config", owner="kk"
+            )
         }
 
     # Packages and systemd units are basically the same with modules as without modules.
@@ -79,10 +84,12 @@ class MyModule(Module):
         return self.pkgs
 
     def user_packages(self) -> list[UserPackage]:
+        # Note, decman now has a aur package, I recommend using that instead.
+        # Also, this example may be out of date
         return [
             UserPackage(
                 pkgname="decman-git",
-                version="0.3.0",
+                version="0.4.1",
                 provides=["decman"],
                 dependencies=[
                     "python",
@@ -106,6 +113,12 @@ class MyModule(Module):
     def aur_packages(self) -> list[str]:
         return ["protonvpn"]
 
+    def flatpak_packages(self) -> list[str]:
+        return ["org.mozilla.firefox"]
+
+    def flatpak_user_packages(self) -> dict[str, list[str]]:
+        return {"username": ["io.github.kolunmi.Bazaar"]}
+
     def systemd_units(self) -> list[str]:
         return ["reflector.timer"]
 

example/source.py

@@ -1,8 +1,8 @@
 # This example covers all decman features and many useful ways of configuring a system.
 # Configuration can be as simple or as complex as is needed.
 
-import socket
 import os
+import socket
 
 # Note: Do NOT use from imports for global variables
 # BAD: from decman import packages/modules/etc
@@ -10,7 +10,10 @@ import decman
 import decman.config
 
 # This is fine since the thing being imported is a class and not a global variable.
-from decman import UserPackage, File, Directory, UserRaisedError
+from decman import Directory, File, UserPackage, UserRaisedError
+
+# Flatpaks are disabled by default. This way no already installed flatpaks will get suddenly deleted.
+decman.config.enable_flatpak = True
 
 # Configuring what packages are installed is easy.
 # Duplicates are OK, so if you have multiple modules that want to ensure a package is installed,
@@ -26,7 +29,19 @@ decman.packages += ["python", "python", "devtools", "git", "networkmanager"]
 decman.ignored_packages += ["rustup", "yay"]
 
 # Installing AUR packages is easy.
-decman.aur_packages += ["protonvpn"]
+decman.aur_packages += ["decman", "protonvpn"]
+
+# Flatpaks work the same way as all other packages.
+decman.flatpak_packages += ["dev.qwery.AddWater"]
+
+# They too can be ignored of course
+decman.ignored_flatpak_packages += ["org.signal.Signal"]
+
+# You can also install them to your user installation instead of the system installation
+# Ensure that previous user installed flatpak declarations aren't overwritten and they are initialized.
+decman.flatpak_user_packages["kk"] = decman.flatpak_user_packages.get("kk", [])
+# Now add the package.
+decman.flatpak_user_packages["kk"].append("dev.zed.Zed")
 
 # To import GPG keys, set the GNUPGHOME environment variable.
 # It can easily be done with python as well.
@@ -36,11 +51,13 @@ decman.config.makepkg_user = "kk"
 
 # You can also install packages from anywhere, but then you must include some
 # information about the package. The git_url is the url to the PKGBUILD,
-# This example may not be up to date, but you should keep these up to date with the PKGBUILD.
+#
+# Note, decman now has a aur package, I recommend using that instead.
+# Also, this example may be out of date
 decman.user_packages.append(
     UserPackage(
         pkgname="decman-git",
-        version="0.3.0",
+        version="0.4.1",
         provides=["decman"],
         dependencies=[
             "python",
@@ -58,7 +75,8 @@ decman.user_packages.append(
             "python-wheel",
         ],
         git_url="https://github.com/kiviktnm/decman-pkgbuild.git",
-    ))
+    )
+)
 
 # Managing only packages with decman is not that interesting.
 # Decman also has really powerful ways of managing config files, scripts etc.
@@ -68,23 +86,25 @@ decman.user_packages.append(
 
 # Define file content inline.
 # Default text file encoding is utf-8 but it can be changed.
-decman.files["/etc/vconsole.conf"] = File(content="KEYMAP=us",
+decman.files["/etc/vconsole.conf"] = File(content="KEYMAP=us", encoding="utf-8")
-                                          encoding="utf-8")
 
 # Include file content from another file, set the file owner and permissions.
 # The source_file is relative to the directory where the main decman source.py is located.
 # By default, the file group is set to the group of the owner, but it can be overridden with the group argument.
 decman.files["/home/kk/.bin/user-script.sh"] = File(
-    source_file="files/user-script.sh", owner="kk", permissions=0o744)
+    source_file="files/user-script.sh", owner="kk", permissions=0o744
+)
 
 # Non-text files such as images can also be managed.
 decman.files["/home/kk/.background.png"] = File(
-    source_file="files/i-dont-actually-exist.png", bin_file=True, owner="kk")
+    source_file="files/i-dont-actually-exist.png", bin_file=True, owner="kk"
+)
 
 # If you need to install multiple files at once, use directories.
 # All files from the source directory will be copied recursively to the target.
 decman.directories["/home/kk/.config/app/"] = Directory(
-    source_directory="files/app-config", owner="kk")
+    source_directory="files/app-config", owner="kk"
+)
 
 # Decman has built in support for managing systemd units as well.
 # Decman will enable services declared here, and disable services removed from here.
@@ -95,8 +115,9 @@ decman.enabled_systemd_units += ["NetworkManager.service"]
 # You can manage units for users as well.
 
 # Ensure that previous user unit declarations aren't overwritten and they are initialized.
-decman.enabled_systemd_user_units[
+decman.enabled_systemd_user_units["kk"] = decman.enabled_systemd_user_units.get(
-    "kk"] = decman.enabled_systemd_user_units.get("kk", [])
+    "kk", []
+)
 # Add user unit.
 decman.enabled_systemd_user_units["kk"].append("syncthing.service")
 
@@ -141,9 +162,9 @@ decman.config.pacman_output_keywords = [
     "pacsave",
     "pacnew",
     # Additional keywords can be:
-    #"warning",
+    # "warning",
-    #"error",
+    # "error",
-    #"note",
+    # "note",
     # They might cause too many highlights however.
 ]
 # If you don't want to print lines that contain keywords, set this to False
@@ -173,7 +194,6 @@ decman.config.number_of_packages_stored_in_cache = 3
 # Create a child class of the decman.config.Commands class and override methods.
 # These are the defaults.
 class MyCommands(decman.config.Commands):
-
     def list_pkgs(self) -> list[str]:
         return ["pacman", "-Qeq", "--color=never"]
 
@@ -193,8 +213,7 @@ class MyCommands(decman.config.Commands):
         return ["pacman", "-D", "--asexplicit"] + pkgs
 
     def install_deps(self, deps: list[str]) -> list[str]:
-        return ["pacman", "-S", "--color=always", "--needed", "--asdeps"
+        return ["pacman", "-S", "--color=always", "--needed", "--asdeps"] + deps
-                ] + deps
 
     def is_installable(self, pkg: str) -> list[str]:
         return ["pacman", "-Sddp", pkg]
@@ -217,8 +236,7 @@ class MyCommands(decman.config.Commands):
     def disable_user_units(self, units: list[str], user: str) -> list[str]:
         return ["systemctl", "--user", "-M", f"{user}@", "disable"] + units
 
-    def compare_versions(self, installed_version: str,
+    def compare_versions(self, installed_version: str, new_version: str) -> list[str]:
-                         new_version: str) -> list[str]:
         return ["vercmp", installed_version, new_version]
 
     def git_clone(self, repo: str, dest: str) -> list[str]:
@@ -230,6 +248,9 @@ class MyCommands(decman.config.Commands):
     def git_get_commit_id(self) -> list[str]:
         return ["git", "rev-parse", "HEAD"]
 
+    def git_log_commit_ids(self) -> list[str]:
+        return ["git", "log", "--format=format:%H"]
+
     def review_file(self, file: str) -> list[str]:
         return ["less", file]
 
@@ -238,20 +259,32 @@ class MyCommands(decman.config.Commands):
 
     def install_chroot_packages(self, chroot_dir: str, packages: list[str]):
         return [
-            "arch-nspawn", chroot_dir, "pacman", "-S", "--needed",
+            "arch-nspawn",
-            "--noconfirm"
+            chroot_dir,
+            "pacman",
+            "-S",
+            "--needed",
+            "--noconfirm",
         ] + packages
 
-    def remove_chroot_packages(self, chroot_dir: str, packages: list[str]):
+    def resolve_real_name(self, chroot_dir: str, pkg: str) -> list[str]:
-        return ["arch-nspawn", chroot_dir, "pacman", "-Rsu", "--noconfirm"
+        return [
-                ] + packages
+            "arch-nspawn",
-
+            chroot_dir,
-    def make_chroot_pkg(self, chroot_wd_dir: str, user: str,
+            "pacman",
-                        pkgfiles_to_install: list[str]) -> list[str]:
+            "-Sddp",
-        makechrootpkg_cmd = [
+            "--print-format=%n",
-            "makechrootpkg", "-c", "-r", chroot_wd_dir, "-U", user
+            pkg,
         ]
 
+    def remove_chroot_packages(self, chroot_dir: str, packages: list[str]):
+        return ["arch-nspawn", chroot_dir, "pacman", "-Rsu", "--noconfirm"] + packages
+
+    def make_chroot_pkg(
+        self, chroot_wd_dir: str, user: str, pkgfiles_to_install: list[str]
+    ) -> list[str]:
+        makechrootpkg_cmd = ["makechrootpkg", "-c", "-r", chroot_wd_dir, "-U", user]
+
         for pkgfile in pkgfiles_to_install:
             makechrootpkg_cmd += ["-I", pkgfile]
 
@@ -267,7 +300,6 @@ decman.config.commands = MyCommands()
 
 
 class PikaurWrapperCommands(decman.config.Commands):
-
     def list_pkgs(self) -> list[str]:
         return ["pikaur", "-Qeq"]
 

pyproject.toml

@@ -4,15 +4,21 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "decman"
-version = "0.3.0"
+version = "0.4.1"
 description = "Declarative package & configuration manager for Arch Linux."
 license = {file = "LICENSE"}
 authors = [
     {name = "Kivi Kaitaniemi"}
 ]
 dependencies = [
-    "requests"
+    "requests",
 ]
 
 [project.scripts]
 decman = "decman.app:main"
+
+[dependency-groups]
+dev = [
+    "isort>=5.13.2",
+    "ruff>=0.9.3",
+]

src/decman/__init__.py

@@ -2,12 +2,13 @@
 Module for writing system configurations for decman.
 """
 
-import typing
-import pwd
 import grp
-import shutil
 import os
+import pwd
+import shutil
 import subprocess
+import typing
+
 import decman.error
 
 
@@ -20,9 +21,11 @@ class UserRaisedError(Exception):
         super().__init__(message)
 
 
-def sh(sh_cmd: str,
+def sh(
-       user: typing.Optional[str] = None,
+    sh_cmd: str,
-       env_overrides: typing.Optional[dict[str, str]] = None):
+    user: typing.Optional[str] = None,
+    env_overrides: typing.Optional[dict[str, str]] = None,
+):
     """
     Shortcut for running a shell command.
     """
@@ -49,16 +52,20 @@ def sh(sh_cmd: str,
                 f"Running user defined shell command failed because the user {user} doesn't exist."
             ) from e
 
-        with subprocess.Popen(sh_cmd, shell=True, group=gid, user=uid,
+        with subprocess.Popen(
-                              env=env) as process:
+            sh_cmd, shell=True, group=gid, user=uid, env=env
+        ) as process:
             if process.wait() != 0:
                 raise decman.error.UserFacingError(
-                    f"Running user shell command '{sh_cmd}' as {user} failed.")
+                    f"Running user shell command '{sh_cmd}' as {user} failed."
+                )
 
 
-def prg(command: list[str],
+def prg(
-        user: typing.Optional[str] = None,
+    command: list[str],
-        env_overrides: typing.Optional[dict[str, str]] = None):
+    user: typing.Optional[str] = None,
+    env_overrides: typing.Optional[dict[str, str]] = None,
+):
     """
     Shortcut for running a program.
     """
@@ -74,7 +81,8 @@ def prg(command: list[str],
             subprocess.run(command, check=True, env=env)
         except subprocess.CalledProcessError as e:
             raise decman.error.UserFacingError(
-                f"Running user defined program '{command}' failed.") from e
+                f"Running user defined program '{command}' failed."
+            ) from e
     else:
         try:
             uid = pwd.getpwnam(user).pw_uid
@@ -84,11 +92,11 @@ def prg(command: list[str],
                 f"Running user defined program failed because the user {user} doesn't exist."
             ) from e
 
-        with subprocess.Popen(command, group=gid, user=uid,
+        with subprocess.Popen(command, group=gid, user=uid, env=env) as process:
-                              env=env) as process:
             if process.wait() != 0:
                 raise decman.error.UserFacingError(
-                    f"Running user program '{command}' as {user} failed.")
+                    f"Running user program '{command}' as {user} failed."
+                )
 
 
 class File:
@@ -127,9 +135,7 @@ class File:
         if group is not None:
             self.gid = grp.getgrnam(group).gr_gid
 
-    def copy_to(self,
+    def copy_to(self, target: str, variables: typing.Optional[dict[str, str]] = None):
-                target: str,
-                variables: typing.Optional[dict[str, str]] = None):
         """
         Copies the contents of this file to the target file.
         """
@@ -138,8 +144,9 @@ class File:
 
         target_directory = os.path.dirname(target)
 
-        def create_missing_dirs(dirct: str, uid: typing.Optional[int],
+        def create_missing_dirs(
-                                gid: typing.Optional[int]):
+            dirct: str, uid: typing.Optional[int], gid: typing.Optional[int]
+        ):
             if not os.path.isdir(dirct):
                 parent_dir = os.path.dirname(dirct)
                 if not os.path.isdir(parent_dir):
@@ -161,8 +168,7 @@ class File:
         os.chmod(target, self.permissions)
 
     def _write_content(self, target: str, variables: dict[str, str]):
-        if self.source_file is not None and (self.bin_file
+        if self.source_file is not None and (self.bin_file or len(variables) == 0):
-                                             or len(variables) == 0):
             shutil.copy(self.source_file, target)
         elif self.bin_file and self.content is not None:
             with open(target, "wb") as file:
@@ -177,7 +183,9 @@ class File:
             with open(target, "wt", encoding=self.encoding) as file:
                 file.write(content)
         else:
-            assert self.content is not None, "Content should be set since source_file was not set."
+            assert self.content is not None, (
+                "Content should be set since source_file was not set."
+            )
             content = self.content
             for var, value in variables.items():
                 content = content.replace(var, value)
@@ -217,10 +225,12 @@ class Directory:
         if group is not None:
             self.gid = grp.getgrnam(group).gr_gid
 
-    def copy_to(self,
+    def copy_to(
-                target_directory: str,
+        self,
-                variables: typing.Optional[dict[str, str]] = None,
+        target_directory: str,
-                only_print: bool = False) -> list[str]:
+        variables: typing.Optional[dict[str, str]] = None,
+        only_print: bool = False,
+    ) -> list[str]:
         """
         Copies the files in this directory to the target directory.
 
@@ -233,14 +243,15 @@ class Directory:
             for src_dir, _, src_files in os.walk("."):
                 for src_file in src_files:
                     src_path = os.path.join(src_dir, src_file)
-                    file = File(source_file=src_path,
+                    file = File(
-                                bin_file=self.bin_files,
+                        source_file=src_path,
-                                encoding=self.encoding,
+                        bin_file=self.bin_files,
-                                owner=self.owner,
+                        encoding=self.encoding,
-                                group=self.group,
+                        owner=self.owner,
-                                permissions=self.permissions)
+                        group=self.group,
-                    target = os.path.normpath(
+                        permissions=self.permissions,
-                        os.path.join(target_directory, src_path))
+                    )
+                    target = os.path.normpath(os.path.join(target_directory, src_path))
                     created.append(target)
 
                     if not only_print:
@@ -369,6 +380,20 @@ class Module:
         """
         return []
 
+    def flatpak_packages(self) -> list[str]:
+        """
+        Override this method to return flatpak packages that should be installed to the system installation as a part of this
+        Module.
+        """
+        return []
+
+    def flatpak_user_packages(self) -> dict[str, list[str]]:
+        """
+        Override this method to return flatpak packages that should be installed to the user installation as a part of this
+        Module.
+        """
+        return {}
+
     def systemd_units(self) -> list[str]:
         """
         Override this method to return systemd units that should be enabled as a part of this
@@ -401,3 +426,6 @@ enabled_systemd_user_units: dict[str, list[str]] = {}
 files: dict[str, File] = {}
 directories: dict[str, Directory] = {}
 modules: list[Module] = []
+flatpak_packages: list[str] = []
+flatpak_user_packages: dict[str, list[str]] = {}
+ignored_flatpak_packages: list[str] = []

src/decman/app.py

@@ -1,16 +1,19 @@
+# pyright: reportUnusedCallResult=false
 """
 Module containing the CLI Application.
 """
 
 import argparse
 import os
+import pwd
+import shutil
 import sys
 import traceback
 
 import decman
+import decman.config as conf
 import decman.error as err
 import decman.lib as l
-import decman.config as conf
 from decman.lib import fpm
 
 
@@ -23,53 +26,68 @@ def main():
 
     parser = argparse.ArgumentParser(
         prog="decman",
-        description=
+        description="Declarative package & configuration manager for Arch Linux",
-        "Declarative package & configuration manager for Arch Linux",
+        epilog="See more help at: https://github.com/kiviktnm/decman",
-        epilog="See more help at: https://github.com/kiviktnm/decman")
+    )
 
-    parser.add_argument("--source",
+    parser.add_argument(
-                        action="store",
+        "--source", action="store", help="python file containing configuration"
-                        help="python file containing configuration")
+    )
     parser.add_argument(
         "--print",
         "--dry-run",
         action="store_true",
         default=False,
-        help="print what would happen as a result of running decman")
+        help="print what would happen as a result of running decman",
-    parser.add_argument("--debug",
+    )
-                        action="store_true",
+    parser.add_argument(
-                        default=False,
+        "--debug", action="store_true", default=False, help="show debug output"
-                        help="show debug output")
+    )
     parser.add_argument(
         "--no-packages",
         action="store_true",
         default=False,
-        help="don't upgrade any packages (including foreign packages)")
+        help="don't upgrade any packages (including foreign packages)",
-    parser.add_argument("--no-foreign-packages",
+    )
-                        action="store_true",
+    parser.add_argument(
-                        default=False,
+        "--no-foreign-packages",
-                        help="don't upgrade foreign packages")
+        action="store_true",
-    parser.add_argument("--no-files",
+        default=False,
-                        action="store_true",
+        help="don't upgrade foreign packages",
-                        default=False,
+    )
-                        help="don't install any files")
+    parser.add_argument(
-    parser.add_argument("--no-systemd-units",
+        "--no-flatpaks",
-                        action="store_true",
+        action="store_true",
-                        default=False,
+        default=False,
-                        help="don't enable/disable systemd units")
+        help="don't upgrade flatpak packages",
-    parser.add_argument("--no-commands",
+    )
-                        action="store_true",
+    parser.add_argument(
-                        default=False,
+        "--no-files", action="store_true", default=False, help="don't install any files"
-                        help="don't run user specified commands")
+    )
-    parser.add_argument("--upgrade-devel",
+    parser.add_argument(
-                        action="store_true",
+        "--no-systemd-units",
-                        default=False,
+        action="store_true",
-                        help="upgrade devel packages")
+        default=False,
+        help="don't enable/disable systemd units",
+    )
+    parser.add_argument(
+        "--no-commands",
+        action="store_true",
+        default=False,
+        help="don't run user specified commands",
+    )
+    parser.add_argument(
+        "--upgrade-devel",
+        action="store_true",
+        default=False,
+        help="upgrade devel packages",
+    )
     parser.add_argument(
         "--force-build",
         action="store_true",
         default=False,
-        help="force building of packages that are already cached")
+        help="force building of packages that are already cached",
+    )
 
     args = parser.parse_args()
 
@@ -105,8 +123,7 @@ def main():
             l.print_debug(line)
         errored = True
     except decman.UserRaisedError as user_error:
-        l.print_error(
+        l.print_error(f"Error encountered while running the source: {user_error}")
-            f"Error encountered while running the source: {user_error}")
         errored = True
 
     # Save even when an error has occurred, since this avoids repeating steps like building pkgs.
@@ -158,13 +175,24 @@ def _set_up(store: l.Store, args):
             content = file.read()
     except OSError as e:
         raise err.UserFacingError(
-            f"Failed to read source file '{store.source_file}'.") from e
+            f"Failed to read source file '{store.source_file}'."
+        ) from e
 
     os.chdir(source_dir)
     sys.path.append(".")
     exec(content)
 
-    return args.print, not args.no_packages, not args.no_foreign_packages, not args.no_files, not args.no_systemd_units, not args.no_commands, args.upgrade_devel, args.force_build
+    return (
+        args.print,
+        not args.no_packages,
+        not args.no_foreign_packages,
+        not args.no_flatpaks,
+        not args.no_files,
+        not args.no_systemd_units,
+        not args.no_commands,
+        args.upgrade_devel,
+        args.force_build,
+    )
 
 
 class Core:
@@ -173,25 +201,43 @@ class Core:
     """
 
     def __init__(self, store: l.Store, opts):
-        self.only_print, self.update_packages, self.update_foreign_packages, self.update_files, self.update_units, self.run_commands, self.upgrade_devel, self.force_build = opts
+        (
+            self.only_print,
+            self.update_packages,
+            self.update_foreign_packages,
+            self.update_flatpaks,
+            self.update_files,
+            self.update_units,
+            self.run_commands,
+            self.upgrade_devel,
+            self.force_build,
+        ) = opts
+
+        if conf.enable_flatpak and not shutil.which("flatpak"):
+            l.print_error(
+                "Flatpaks have been enabled in the source file, but the flatpak command could not be found. Either disable flatpaks or make sure that flatpak is installed and can be accessed by decman. Exiting."
+            )
+            sys.exit(1)
 
         self.store = store
         self.source = _resolve_source()
         self.pacman = l.Pacman()
+        self.flatpak = l.Flatpak()
         self.systemctl = l.Systemd(store)
         self.fpkg_search = fpm.ExtendedPackageSearch(self.pacman)
 
         for upkg in self.source.all_user_pkgs():
             self.fpkg_search.add_user_pkg(
-                fpm.PackageInfo.from_user_package(upkg, self.pacman))
+                fpm.PackageInfo.from_user_package(upkg, self.pacman)
+            )
 
-        self.fpm = fpm.ForeignPackageManager(store, self.pacman,
+        self.fpm = fpm.ForeignPackageManager(store, self.pacman, self.fpkg_search)
-                                             self.fpkg_search)
 
     def run(self):
         """
         Run the main logic of decman.
         """
+
         if self.update_units:
             self._disable_units()
 
@@ -218,6 +264,8 @@ class Core:
     def _disable_units(self):
         to_disable = self.source.units_to_disable(self.store)
         l.print_list("Disabling systemd units:", to_disable)
+        if to_disable:
+            l.print_info("Disabled systemd units won't be stopped automatically.")
         if not self.only_print:
             self.systemctl.disable_units(to_disable)
 
@@ -228,26 +276,105 @@ class Core:
                 self.systemctl.disable_user_units(units, user)
 
     def _remove_pkgs(self):
+        """
+        Remove pacman and flatpak packages
+        """
+        # pacman
         currently_installed = self.pacman.get_installed()
         to_remove = self.source.packages_to_remove(currently_installed)
-        l.print_list("Removing packages:", to_remove)
+
-        if not self.only_print:
+        currently_installed_flatpak = self.flatpak.get_installed()
-            self.pacman.remove(to_remove)
+        to_remove_flatpak = self.source.flatpak_packages_to_remove(
+            currently_installed_flatpak
+        )
+
+        l.print_list("Removing pacman packages:", to_remove)
+
+        if conf.enable_flatpak and self.update_flatpaks:
+            l.print_list("Removing flatpak packages:", to_remove_flatpak)
+            self._remove_user_flatpaks(only_print=True)
+
+        if self.only_print:
+            return
+
+        self.pacman.remove(to_remove)
+
+        # flatpak
+        if conf.enable_flatpak and self.update_flatpaks:
+            self.flatpak.remove(to_remove_flatpak)
+            self._remove_user_flatpaks()
+
+    def _remove_user_flatpaks(self, only_print: bool = False):
+        # Get all non system users (users that have uid >= 1000), also ignore nobody
+        users = [
+            u.pw_name
+            for u in pwd.getpwall()
+            if u.pw_uid >= 1000 and u.pw_name not in ("nobody",)
+        ]
+        # Add root to users
+        users.append("root")
+        for user in users:
+            currently_installed_flatpak = self.flatpak.get_installed(
+                as_user=True, which_user=user
+            )
+            to_remove_flatpak = self.source.flatpak_packages_to_remove(
+                currently_installed_flatpak, as_user=True, which_user=user
+            )
+            l.print_list(
+                f"Removing flatpak packages from user installation for user {user}",
+                to_remove_flatpak,
+            )
+
+            if only_print:
+                continue
+
+            self.flatpak.remove(to_remove_flatpak, True, user)
 
     def _upgrade_pkgs(self):
+        """
+        Upgrade pacman, fpm and flatpak packages
+        """
+        # flatpak + fpm
         l.print_summary("Upgrading packages.")
-        if not self.only_print:
+        if self.only_print:
-            self.pacman.upgrade()
+            return
-            if conf.enable_fpm and self.update_foreign_packages:
+
-                self.fpm.upgrade(self.upgrade_devel, self.force_build,
+        self.pacman.upgrade()
-                                 self.source.ignored_packages)
+        if conf.enable_fpm and self.update_foreign_packages:
+            self.fpm.upgrade(
+                self.upgrade_devel, self.force_build, self.source.ignored_packages
+            )
+
+        # flatpak
+        if conf.enable_flatpak and self.update_flatpaks:
+            l.print_summary("Upgrading flatpak packages.")
+            self.flatpak.upgrade()
+            users = [
+                u.pw_name
+                for u in pwd.getpwall()
+                if u.pw_uid >= 1000 and u.pw_name not in ("nobody",)
+            ]
+            # Add root to users
+            users.append("root")
+            for user in users:
+                l.print_summary(f"Upgrading flatpak packages for {user}.")
+                self.flatpak.upgrade(True, user)
 
     def _install_pkgs(self):
+        """
+        Installs all pacman, fpm, and flatpak packages.
+        """
+
+        # pacman + fpm
         currently_installed = self.pacman.get_installed()
-        to_install_pacman = self.source.pacman_packages_to_install(
+        to_install_pacman = self.source.pacman_packages_to_install(currently_installed)
-            currently_installed)
+        to_install_fpm = self.source.foreign_packages_to_install(currently_installed)
-        to_install_fpm = self.source.foreign_packages_to_install(
+
-            currently_installed)
+        # flatpak
+        currently_installed_flatpak = self.flatpak.get_installed()
+        to_install_flatpak = self.source.flatpak_packages_to_install(
+            currently_installed_flatpak
+        )
 
         l.print_list("Installing pacman packages:", to_install_pacman)
 
@@ -255,10 +382,48 @@ class Core:
         if self.only_print:
             l.print_list("Installing foreign packages:", to_install_fpm)
 
-        if not self.only_print:
+        if conf.enable_flatpak and self.update_flatpaks:
-            self.pacman.install(to_install_pacman)
+            l.print_list("Installing flatpak packages:", to_install_flatpak)
-            if conf.enable_fpm and self.update_foreign_packages:
+
-                self.fpm.install(to_install_fpm, force=self.force_build)
+        if self.only_print:
+            self._install_user_flatpaks(only_print=True)
+            return
+
+        self.pacman.install(to_install_pacman)
+        if conf.enable_fpm and self.update_foreign_packages:
+            self.fpm.install(to_install_fpm, force=self.force_build)
+
+        if conf.enable_flatpak and self.update_flatpaks:
+            self.flatpak.install(to_install_flatpak)
+            # Print summary before the action
+            self._install_user_flatpaks(only_print=True)
+            self._install_user_flatpaks()
+
+    def _install_user_flatpaks(self, only_print: bool = False):
+        # Get all non system users (users that have uid >= 1000), also ignore nobody
+        users = [
+            u.pw_name
+            for u in pwd.getpwall()
+            if u.pw_uid >= 1000 and u.pw_name not in ("nobody",)
+        ]
+        # Add root to users
+        users.append("root")
+        for user in users:
+            currently_installed_flatpak = self.flatpak.get_installed(
+                as_user=True, which_user=user
+            )
+            to_install_flatpak = self.source.flatpak_packages_to_install(
+                currently_installed_flatpak, as_user=True, which_user=user
+            )
+
+            if only_print:
+                l.print_list(
+                    f"Installing flatpak packages to user installation for user {user}",
+                    to_install_flatpak,
+                )
+                continue
+
+            self.flatpak.install(to_install_flatpak, True, user)
 
     def _create_and_remove_files(self):
         l.print_summary("Installing files.")
@@ -266,9 +431,7 @@ class Core:
         all_created = self.source.create_all_files(self.only_print)
         to_remove = self.source.files_to_remove(self.store, all_created)
 
-        l.print_list("Ensured files are up to date:",
+        l.print_list("Ensured files are up to date:", all_created, elements_per_line=1)
-                     all_created,
-                     elements_per_line=1)
         l.print_list("Removing files:", to_remove, elements_per_line=1)
 
         if self.only_print:
@@ -286,6 +449,8 @@ class Core:
     def _enable_units(self):
         to_enable = self.source.units_to_enable(self.store)
         l.print_list("Enabling systemd units:", to_enable)
+        if to_enable:
+            l.print_info("Enabled systemd units won't be started automatically.")
         if not self.only_print:
             self.systemctl.enable_units(to_enable)
 
@@ -318,6 +483,10 @@ def _resolve_source() -> l.Source:
     for user, units in decman.enabled_systemd_user_units.items():
         enabled_systemd_user_units[user] = set(units)
 
+    flatpak_user_packages = {}
+    for user, pkgs in decman.flatpak_user_packages.items():
+        flatpak_user_packages[user] = set(pkgs)
+
     return l.Source(
         pacman_packages=set(decman.packages),
         aur_packages=set(decman.aur_packages),
@@ -328,6 +497,9 @@ def _resolve_source() -> l.Source:
         files=decman.files,
         directories=decman.directories,
         modules=set(decman.modules),
+        flatpak_packages=set(decman.flatpak_packages),
+        flatpak_user_packages=flatpak_user_packages,
+        ignored_flatpak_packages=set(decman.ignored_flatpak_packages),
     )
 
 

src/decman/config.py

@@ -34,6 +34,20 @@ class Commands:
         """
         return ["pacman", "-Qeq", "--color=never"]
 
+    def list_flatpak_pkgs(self, as_user: bool = False) -> list[str]:
+        """
+        Running this command outputs a newline separated list of installed flatpak application ids
+        The first line just says 'Application ID' so this one is ignored.
+        """
+        return [
+            "flatpak",
+            "list",
+            "--app",
+            "--user" if as_user else "--system",
+            "--columns",
+            "application",
+        ]
+
     def list_foreign_pkgs_versioned(self) -> list[str]:
         """
         Running this command outputs a newline seperated list of installed packages and their
@@ -47,6 +61,12 @@ class Commands:
         """
         return ["pacman", "-S", "--color=always", "--needed"] + pkgs
 
+    def install_flatpak_pkgs(self, pkgs: list[str], as_user: bool = False) -> list[str]:
+        """
+        Running this command installs all listed packages, and their dependencies/runtimes automatically.
+        """
+        return ["flatpak", "install", "-y", "--user" if as_user else "--system"] + pkgs
+
     def install_files(self, pkg_files: list[str]) -> list[str]:
         """
         Running this command installs the given packages files.
@@ -64,8 +84,7 @@ class Commands:
         Running this command installs the given packages from pacman repositories.
         The packages are installed as dependencies.
         """
-        return ["pacman", "-S", "--color=always", "--needed", "--asdeps"
+        return ["pacman", "-S", "--color=always", "--needed", "--asdeps"] + deps
-                ] + deps
 
     def is_installable(self, pkg: str) -> list[str]:
         """
@@ -79,6 +98,18 @@ class Commands:
         """
         return ["pacman", "-Syu", "--color=always"]
 
+    def upgrade_flatpak(self, as_user: bool = False) -> list[str]:
+        """
+        Updates all installed flatpak REFs including runtimes and dependencies.
+        """
+        return [
+            "flatpak",
+            "update",
+            "--noninteractive",
+            "-y",
+            "--user" if as_user else "--system",
+        ]
+
     def remove(self, pkgs: list[str]) -> list[str]:
         """
         Running this command removes the given packages and their dependencies
@@ -86,6 +117,31 @@ class Commands:
         """
         return ["pacman", "-Rs", "--color=always"] + pkgs
 
+    def remove_flatpak(self, pkgs: list[str], as_user: bool = False) -> list[str]:
+        """
+        Running this command will remove the listed REFs. Unused dependencies might be kept, but to remove them another command needs to be run.
+        """
+        return [
+            "flatpak",
+            "remove",
+            "--noninteractive",
+            "-y",
+            "--user" if as_user else "--system",
+        ] + pkgs
+
+    def remove_unused_flatpak(self, as_user: bool = False) -> list[str]:
+        """
+        This will remove all unused flatpak dependencies and runtimes.
+        """
+        return [
+            "flatpak",
+            "remove",
+            "--noninteractive",
+            "-y",
+            "--unused",
+            "--user" if as_user else "--system",
+        ]
+
     def enable_units(self, units: list[str]) -> list[str]:
         """
         Running this command enables the given systemd units.
@@ -110,8 +166,7 @@ class Commands:
         """
         return ["systemctl", "--user", "-M", f"{user}@", "disable"] + units
 
-    def compare_versions(self, installed_version: str,
+    def compare_versions(self, installed_version: str, new_version: str) -> list[str]:
-                         new_version: str) -> list[str]:
         """
         Running this command outputs -1 when the installed version is older than the new version.
         """
@@ -136,6 +191,12 @@ class Commands:
         """
         return ["git", "rev-parse", "HEAD"]
 
+    def git_log_commit_ids(self) -> list[str]:
+        """
+        Running this command outputs commit hashes of the repository.
+        """
+        return ["git", "log", "--format=format:%H"]
+
     def review_file(self, file: str) -> list[str]:
         """
         Running this command outputs a file for the user to see.
@@ -154,27 +215,42 @@ class Commands:
         Running this command installs the given packages to the given chroot.
         """
         return [
-            "arch-nspawn", chroot_dir, "pacman", "-S", "--needed",
+            "arch-nspawn",
-            "--noconfirm"
+            chroot_dir,
+            "pacman",
+            "-S",
+            "--needed",
+            "--noconfirm",
         ] + packages
 
+    def resolve_real_name(self, chroot_dir: str, pkg: str) -> list[str]:
+        """
+        This command prints a real name of a package. For example, it prints the package which provides a virtual package.
+        """
+        return [
+            "arch-nspawn",
+            chroot_dir,
+            "pacman",
+            "-Sddp",
+            "--print-format=%n",
+            pkg,
+        ]
+
     def remove_chroot_packages(self, chroot_dir: str, packages: list[str]):
         """
         Running this command removes the given packages from the given chroot.
         """
-        return ["arch-nspawn", chroot_dir, "pacman", "-Rsu", "--noconfirm"
+        return ["arch-nspawn", chroot_dir, "pacman", "-Rsu", "--noconfirm"] + packages
-                ] + packages
 
-    def make_chroot_pkg(self, chroot_wd_dir: str, user: str,
+    def make_chroot_pkg(
-                        pkgfiles_to_install: list[str]) -> list[str]:
+        self, chroot_wd_dir: str, user: str, pkgfiles_to_install: list[str]
+    ) -> list[str]:
         """
         Running this command creates a package file using the given chroot.
         The package is created as the user and the pkg_files_to_install are installed
         in the chroot before the package is created.
         """
-        makechrootpkg_cmd = [
+        makechrootpkg_cmd = ["makechrootpkg", "-c", "-r", chroot_wd_dir, "-U", user]
-            "makechrootpkg", "-c", "-r", chroot_wd_dir, "-U", user
-        ]
 
         for pkgfile in pkgfiles_to_install:
             makechrootpkg_cmd += ["-I", pkgfile]
@@ -204,9 +280,9 @@ pacman_output_keywords: list[str] = [
     "pacsave",
     "pacnew",
     # These cause too many false positives IMO
-    #"warning",
+    # "warning",
-    #"error",
+    # "error",
-    #"note",
+    # "note",
 ]
 print_pacman_output_highlights: bool = True
 
@@ -215,4 +291,5 @@ build_dir: str = "/tmp/decman/build"
 pkg_cache_dir: str = "/var/cache/decman"
 aur_rpc_timeout: typing.Optional[int] = 30
 enable_fpm: bool = True
+enable_flatpak: bool = False
 number_of_packages_stored_in_cache: int = 3

src/decman/lib/__init__.py

@@ -2,17 +2,18 @@
 Library module for decman.
 """
 
-import threading
-import sys
-import shutil
-import subprocess
 import json
 import os
-import typing
+import pty
+import pwd
+import shutil
+import subprocess
 import time
+import typing
+
+import decman
 import decman.config as conf
 import decman.error as err
-import decman
 
 _DECMAN_MSG_TAG = "[\033[1;35mDECMAN\033[m]"
 _RED_PREFIX = "\033[91m"
@@ -60,12 +61,14 @@ def print_summary(msg: str):
     print(f"{_DECMAN_MSG_TAG} {_CYAN_PREFIX}SUMMARY{_RESET_SUFFIX}: {msg}")
 
 
-def print_list(msg: str,
+def print_list(
-               l: list[str],
+    msg: str,
-               elements_per_line: typing.Optional[int] = None,
+    l: list[str],
-               max_line_width: typing.Optional[int] = None,
+    elements_per_line: typing.Optional[int] = None,
-               limit_to_term_size: bool = True,
+    max_line_width: typing.Optional[int] = None,
-               level: int = SUMMARY):
+    limit_to_term_size: bool = True,
+    level: int = SUMMARY,
+):
     """
     Prints a summary message to the user along with a list of elements.
 
@@ -89,8 +92,11 @@ def print_list(msg: str,
         max_line_width = 2**32  # Big enough to basically be unlimited
 
     if limit_to_term_size:
-        max_line_width = shutil.get_terminal_size().columns - len(
+        max_line_width = (
-            _SPACING) - len(_CONTINUATION_PREFIX)
+            shutil.get_terminal_size().columns
+            - len(_SPACING)
+            - len(_CONTINUATION_PREFIX)
+        )
 
     lines = [f"{l.pop(0)}"]
     index = 0
@@ -131,10 +137,9 @@ def print_debug(msg: str):
         print(f"{_DECMAN_MSG_TAG} {_GRAY_PREFIX}DEBUG{_RESET_SUFFIX}: {msg}")
 
 
-def prompt_number(msg: str,
+def prompt_number(
-                  min_num: int,
+    msg: str, min_num: int, max_num: int, default: typing.Optional[int] = None
-                  max_num: int,
+) -> int:
-                  default: typing.Optional[int] = None) -> int:
     """
     Prompts the user for a integer.
     """
@@ -263,11 +268,12 @@ class Store:
         if latest_path is None:
             return None
 
-        assert latest_version is not None, "If latest_path is set, then latest_version is set."
+        assert latest_version is not None, (
+            "If latest_path is set, then latest_version is set."
+        )
         return (latest_version, latest_path)
 
-    def add_package_to_cache(self, package: str, version: str,
+    def add_package_to_cache(self, package: str, version: str, path_to_built_pkg: str):
-                             path_to_built_pkg: str):
         """
         Adds a built package to the package file cache. Tries to remove excess cached packages.
         """
@@ -332,14 +338,13 @@ class Store:
 
         d = {
             "source_file": self.source_file,
-            "allow_running_source_without_prompt":
+            "allow_running_source_without_prompt": self.allow_running_source_without_prompt,
-            self.allow_running_source_without_prompt,
             "enabled_systemd_units": self.enabled_systemd_units,
             "enabled_user_systemd_units": self._enabled_user_systemd_units,
             "enabled_modules": self.enabled_modules,
             "created_files": self.created_files,
             "package_file_cache": self._package_file_cache,
-            "pkgbuild_git_commits": self.pkgbuild_latest_reviewed_commits
+            "pkgbuild_git_commits": self.pkgbuild_latest_reviewed_commits,
         }
 
         try:
@@ -370,7 +375,8 @@ class Store:
 
                 store.source_file = d.get("source_file", None)
                 store.allow_running_source_without_prompt = d.get(
-                    "allow_running_source_without_prompt", False)
+                    "allow_running_source_without_prompt", False
+                )
                 store.enabled_systemd_units = d.get(
                     "enabled_systemd_units",
                     [],
@@ -390,12 +396,10 @@ class Store:
             return store
         except json.JSONDecodeError as e:
             print_error(f"{e}")
-            raise err.UserFacingError(
+            raise err.UserFacingError("Failed to parse decman store json.") from e
-                "Failed to parse decman store json.") from e
         except OSError as e:
             print_error(f"{e}")
-            raise err.UserFacingError(
+            raise err.UserFacingError("Failed to read saved decman store.") from e
-                "Failed to read saved decman store.") from e
 
 
 class Source:
@@ -414,6 +418,9 @@ class Source:
         files: dict[str, decman.File],
         directories: dict[str, decman.Directory],
         modules: set[decman.Module],
+        flatpak_packages: set[str],
+        flatpak_user_packages: dict[str, set[str]],
+        ignored_flatpak_packages: set[str],
     ):
         self.pacman_packages = pacman_packages
         self.aur_packages = aur_packages
@@ -424,6 +431,9 @@ class Source:
         self.files = files
         self.directories = directories
         self.modules = modules
+        self.flatpak_packages = flatpak_packages
+        self.flatpak_user_packages = flatpak_user_packages
+        self.ignored_flatpak_packages = ignored_flatpak_packages
 
     def run_on_enable(self, store: Store):
         """
@@ -455,7 +465,8 @@ class Source:
         """
         for module in self.modules:
             if module.enabled and module.version != store.enabled_modules.get(
-                    module.name, module.version):
+                module.name, module.version
+            ):
                 module.after_version_change()
             elif module.enabled and module.name not in store.enabled_modules:
                 module.after_version_change()
@@ -467,8 +478,10 @@ class Source:
         """
         created_files = []
 
-        def install_files(files: dict[str, decman.File],
+        def install_files(
-                          variables: typing.Optional[dict[str, str]] = None):
+            files: dict[str, decman.File],
+            variables: typing.Optional[dict[str, str]] = None,
+        ):
             for target, file in files.items():
                 created_files.append(target)
 
@@ -481,19 +494,24 @@ class Source:
                 except OSError as e:
                     print_error(f"{e}")
                     raise err.UserFacingError(
-                        f"Failed to install file to {target}.") from e
+                        f"Failed to install file to {target}."
+                    ) from e
 
-        def install_dirs(dirs: dict[str, decman.Directory],
+        def install_dirs(
-                         variables: typing.Optional[dict[str, str]] = None):
+            dirs: dict[str, decman.Directory],
+            variables: typing.Optional[dict[str, str]] = None,
+        ):
             for target, directory in dirs.items():
                 try:
                     print_debug(f"Installing directory to {target}.")
                     created_files.extend(
-                        directory.copy_to(target, variables, only_print))
+                        directory.copy_to(target, variables, only_print)
+                    )
                 except OSError as e:
                     print_error(f"{e}")
                     raise err.UserFacingError(
-                        f"Failed to install directory to {target}.") from e
+                        f"Failed to install directory to {target}."
+                    ) from e
 
         install_files(self.files)
         install_dirs(self.directories)
@@ -531,8 +549,7 @@ class Source:
 
         return all_dirs
 
-    def files_to_remove(self, store: Store,
+    def files_to_remove(self, store: Store, created_files: list[str]) -> list[str]:
-                        created_files: list[str]) -> list[str]:
         """
         Returns all files that should be removed.
         """
@@ -587,8 +604,7 @@ class Source:
                 result[user] = entry
         return result
 
-    def packages_to_remove(
+    def packages_to_remove(self, currently_installed_packages: list[str]) -> list[str]:
-            self, currently_installed_packages: list[str]) -> list[str]:
         """
         Returns all packages that should be removed. This includes pacman, aur and user packages.
         """
@@ -601,7 +617,8 @@ class Source:
         return result
 
     def pacman_packages_to_install(
-            self, currently_installed_packages: list[str]) -> list[str]:
+        self, currently_installed_packages: list[str]
+    ) -> list[str]:
         """
         Returns all pacman packages that should be installed.
         """
@@ -614,7 +631,8 @@ class Source:
         return result
 
     def foreign_packages_to_install(
-            self, currently_installed_packages: list[str]) -> list[str]:
+        self, currently_installed_packages: list[str]
+    ) -> list[str]:
         """
         Returns all aur and user packages that should be installed.
         """
@@ -626,6 +644,43 @@ class Source:
                 result.append(pkg)
         return result
 
+    def flatpak_packages_to_install(
+        self,
+        currently_installed_packages: list[str],
+        as_user: bool = False,
+        which_user: str = "",
+    ) -> list[str]:
+        """
+        Returns all flatpak packages, that are not installed or ignored
+        """
+
+        result: list[str] = []
+        for pkg in self._all_flatpak_packages(as_user, which_user):
+            if pkg in self.ignored_flatpak_packages:
+                continue
+            if pkg not in currently_installed_packages:
+                result.append(pkg)
+        return result
+
+    def flatpak_packages_to_remove(
+        self,
+        currently_installed_packages: list[str],
+        as_user: bool = False,
+        which_user: str = "",
+    ) -> list[str]:
+        """
+        This returns a list of flatpak app ids, that need to be removed since they are installed but not found in either the list of ignored packages,
+        the list of system packages or the list of user packages that need to be installed.
+        """
+        result: list[str] = []
+        for package in currently_installed_packages:
+            if package in self.ignored_flatpak_packages:
+                continue
+            if package not in self._all_flatpak_packages(as_user, which_user):
+                result.append(package)
+
+        return result
+
     def all_enabled_modules(self) -> list[tuple[str, str]]:
         """
         Returns all enabled modules and their versions.
@@ -655,6 +710,27 @@ class Source:
                 result.update(module.pacman_packages())
         return result
 
+    def _all_flatpak_packages(
+        self, as_user: bool = False, which_user: str = ""
+    ) -> set[str]:
+        # loop through all the user packages and save which ones are owned by the currently selected user
+        current_user_flatpak_packages = self.flatpak_user_packages.get(which_user, [])
+
+        result = set()
+        result.update(
+            self.flatpak_packages if not as_user else current_user_flatpak_packages
+        )
+        for module in self.modules:
+            if not module.enabled:
+                continue
+            result.update(
+                module.flatpak_packages()
+                if not as_user
+                else module.flatpak_user_packages().get(which_user, [])
+            )
+
+        return result
+
     def _all_foreign_pkgs(self) -> set[str]:
         result = set()
         result.update(self.aur_packages)
@@ -680,11 +756,13 @@ class Source:
         return result
 
     def _all_user_units(self) -> dict[str, set[str]]:
-        result = {}
+        result = self.systemd_user_units
-        result.update(self.systemd_user_units)
+        for module in [m for m in self.modules if m.enabled]:
-        for module in self.modules:
+            module_user_units: dict[str, list[str]] = module.systemd_user_units()
-            if module.enabled:
+            for user in module_user_units.keys():
-                result.update(module.systemd_user_units())
+                if user not in result:
+                    result[user] = set()
+                result[user].update(module_user_units[user])
         return result
 
 
@@ -702,11 +780,16 @@ class Pacman:
         """
 
         try:
-            packages = subprocess.run(
+            packages = (
-                conf.commands.list_pkgs(),
+                subprocess.run(
-                check=True,
+                    conf.commands.list_pkgs(),
-                stdout=subprocess.PIPE,
+                    check=True,
-            ).stdout.decode().strip().split('\n')
+                    stdout=subprocess.PIPE,
+                )
+                .stdout.decode()
+                .strip()
+                .split("\n")
+            )
             return packages
         except subprocess.CalledProcessError as error:
             raise err.UserFacingError(
@@ -720,9 +803,12 @@ class Pacman:
         if dep in self._installable:
             return self._installable[dep]
 
-        result = subprocess.run(conf.commands.is_installable(dep),
+        result = (
-                                check=False,
+            subprocess.run(
-                                capture_output=True).returncode == 0
+                conf.commands.is_installable(dep), check=False, capture_output=True
+            ).returncode
+            == 0
+        )
         self._installable[dep] = result
         return result
 
@@ -732,18 +818,23 @@ class Pacman:
         basically AUR packages.
         """
         try:
-            output = subprocess.run(
+            output = (
-                conf.commands.list_foreign_pkgs_versioned(),
+                subprocess.run(
-                check=True,
+                    conf.commands.list_foreign_pkgs_versioned(),
-                stdout=subprocess.PIPE).stdout.decode().strip().split('\n')
+                    check=True,
+                    stdout=subprocess.PIPE,
+                )
+                .stdout.decode()
+                .strip()
+                .split("\n")
+            )
         except subprocess.CalledProcessError as error:
             raise err.UserFacingError(
                 f"Failed to get foreign packages using '{error.cmd}'. Output: {error.stdout}."
             ) from error
 
         try:
-            return [(line.split(" ")[0], line.split(" ")[1])
+            return [(line.split(" ")[0], line.split(" ")[1]) for line in output]
-                    for line in output]
         except IndexError as error:
             raise err.UserFacingError(
                 f"Failed to parse foreign packages from pacman output. Output: {output}"
@@ -757,7 +848,8 @@ class Pacman:
             return
 
         returncode, output = echo_and_capture_command(
-            conf.commands.install_pkgs(packages))
+            conf.commands.install_pkgs(packages)
+        )
         if returncode != 0:
             raise err.UserFacingError(
                 f"Failed to install packages using pacman. Process exited with code {returncode}."
@@ -766,9 +858,11 @@ class Pacman:
             print_highlighted_pacman_messages(output)
 
         try:
-            subprocess.run(conf.commands.set_as_explicitly_installed(packages),
+            subprocess.run(
-                           check=True,
+                conf.commands.set_as_explicitly_installed(packages),
-                           capture_output=conf.suppress_command_output)
+                check=True,
+                capture_output=conf.suppress_command_output,
+            )
         except subprocess.CalledProcessError as error:
             raise err.UserFacingError(
                 "Failed to set packages as explicitly installed using pacman."
@@ -781,8 +875,7 @@ class Pacman:
         if not deps:
             return
 
-        returncode, output = echo_and_capture_command(
+        returncode, output = echo_and_capture_command(conf.commands.install_deps(deps))
-            conf.commands.install_deps(deps))
         if returncode != 0:
             raise err.UserFacingError(
                 f"Failed to install packages as dependencies using pacman. Process exited with code {returncode}."
@@ -799,7 +892,8 @@ class Pacman:
             return
 
         returncode, output = echo_and_capture_command(
-            conf.commands.install_files(files))
+            conf.commands.install_files(files)
+        )
         if returncode != 0:
             raise err.UserFacingError(
                 f"Failed to install package files using pacman. Process exited with code {returncode}."
@@ -812,7 +906,8 @@ class Pacman:
                 subprocess.run(
                     conf.commands.set_as_explicitly_installed(as_explicit),
                     check=True,
-                    capture_output=conf.suppress_command_output)
+                    capture_output=conf.suppress_command_output,
+                )
         except subprocess.CalledProcessError as error:
             if conf.suppress_command_output:
                 print_error("Output:")
@@ -840,8 +935,7 @@ class Pacman:
         if not packages:
             return
 
-        returncode, output = echo_and_capture_command(
+        returncode, output = echo_and_capture_command(conf.commands.remove(packages))
-            conf.commands.remove(packages))
         if returncode != 0:
             raise err.UserFacingError(
                 f"Failed to remove packages using pacman. Process exited with code {returncode}."
@@ -859,7 +953,7 @@ def print_highlighted_pacman_messages(output: str):
     for index, line in enumerate(lines):
         for keyword in conf.pacman_output_keywords:
             if keyword.lower() in line.lower():
-                print_summary(f"lines: {index}-{index+2}")
+                print_summary(f"lines: {index}-{index + 2}")
                 if index >= 1:
                     print_continuation(lines[index - 1])
                 print_continuation(line)
@@ -877,57 +971,166 @@ def echo_and_capture_command(program: list[str]) -> tuple[int, str]:
 
     Returns a tuple containing the return code of the program as well as all output of the program.
     """
-    with subprocess.Popen(program,
-                          stdin=subprocess.PIPE,
-                          stdout=subprocess.PIPE,
-                          stderr=subprocess.STDOUT) as process:
-        os.set_blocking(process.stdout.fileno(), False)
 
-        output_thread = _OutputCapturingThread(process.stdout)
+    output = ""
-        output_thread.start()
 
-        os.set_blocking(sys.stdin.fileno(), False)
+    def read(fd):
+        nonlocal output
+        buffer = os.read(fd, 1024)
+        output += buffer.decode(encoding="utf-8")
+        return buffer
 
-        # Capture stdin and forward it to the process in a non-blocking manner
+    returncode = os.waitstatus_to_exitcode(pty.spawn(program, read))
-        while process.poll() is None:
-            inp = sys.stdin.readline()
 
-            if inp:
+    return (returncode, output)
-                process.stdin.write(inp.encode())
-                process.stdin.flush()
-
-            time.sleep(0.1)
-
-        os.set_blocking(sys.stdin.fileno(), True)
-
-        output_thread.done = True
-        output_thread.join()
-
-        # Capture any output that may not have been yet captured
-        output = output_thread.output
-        missing_output = process.stdout.read()
-        if missing_output:
-            output += missing_output.decode()
-
-        return (process.returncode, output)
 
 
-class _OutputCapturingThread(threading.Thread):
+def get_user_info(username: str) -> tuple[int, int]:
+    info = pwd.getpwnam(username)
+    return (info.pw_uid, info.pw_gid)
 
-    def __init__(self, stream):
-        super().__init__()
-        self._stream = stream
-        self.output = ""
-        self.done = False
 
-    def run(self):
+class Flatpak:
-        while not self.done and not self._stream.closed:
+    def __init__(self) -> None:
-            output = self._stream.read()
+        pass
-            if output:
+
-                output = output.decode()
+    def get_installed(self, as_user: bool = False, which_user: str = "") -> list[str]:
-                self.output += output
+        """
-                print(output, end="")
+        Return all of the installed applications. Dependencies and runtimes are exluded since they will not be explicitly installed and thus flatpak will manage them.
-            time.sleep(0.1)
+        """
+        try:
+            uinfo: tuple[int, int] = (0, 0)
+
+            env = os.environ.copy()
+            user_env = env.copy()
+            user_env["HOME"] = os.path.expanduser(f"~{which_user}")
+
+            if as_user:
+                uinfo = get_user_info(which_user)
+
+            proc = subprocess.run(
+                conf.commands.list_flatpak_pkgs(as_user),
+                check=True,
+                stdout=subprocess.PIPE,
+                user=uinfo[0],
+                group=uinfo[1],
+                env=user_env if as_user else env,
+            )
+            packages = proc.stdout.decode().strip().split("\n")
+
+            # print(
+            #     f"as_user: {as_user}, which_user: {which_user}, uinfo: {uinfo}, stdout: {proc.stdout.decode()}, packages: {packages}"
+            # )
+
+            # The header might be included. It might also not. This will make sure that it is not present.
+            if "Application ID" in packages:
+                packages.remove("Application ID")
+
+            if packages == [""]:
+                return []
+
+            return packages
+        except subprocess.CalledProcessError as error:
+            raise err.UserFacingError(
+                user_facing_msg=f"Failed to get installed flatpak packages using '{error.cmd}'. Output: {error.stdout}."
+            ) from error
+
+    def install(
+        self, packages: list[str], as_user: bool = False, which_user: str = "root"
+    ):
+        """
+        Install the listed flatpak packages.
+        """
+        if not packages:
+            return
+
+        uinfo: tuple[int, int] = (0, 0)
+        if as_user:
+            uinfo = get_user_info(which_user)
+
+        env = os.environ.copy()
+        user_env = env.copy()
+        user_env["HOME"] = os.path.expanduser(f"~{which_user}")
+
+        proc = subprocess.run(
+            conf.commands.install_flatpak_pkgs(packages, as_user),
+            check=True,
+            user=uinfo[0],
+            group=uinfo[1],
+            env=user_env if as_user else env,
+        )
+
+        if proc.returncode != 0:
+            raise err.UserFacingError(
+                f"Failed to install flatpak packages. Process exited with code {proc.returncode}."
+            )
+
+    def upgrade(self, as_user: bool = False, which_user: str = "root") -> None:
+        """
+        Upgrade all flatpak packages.
+        """
+        uinfo: tuple[int, int] = (0, 0)
+        if as_user:
+            uinfo = get_user_info(which_user)
+
+        env = os.environ.copy()
+        user_env = env.copy()
+        user_env["HOME"] = os.path.expanduser(f"~{which_user}")
+
+        proc = subprocess.run(
+            conf.commands.upgrade_flatpak(as_user=True),
+            check=True,
+            user=uinfo[0],
+            group=uinfo[1],
+            env=user_env if as_user else env,
+        )
+        if not proc.returncode == 0:
+            raise err.UserFacingError(
+                f"Failed to upgrade flatpak packages. Process exited with code {proc.returncode}."
+            )
+
+    def remove(
+        self, packages: list[str], as_user: bool = False, which_user: str = "root"
+    ):
+        """
+        Remove all the listed packages and their unused dependecies. This has to happen in two steps.
+        """
+        if not packages:
+            return
+
+        uinfo: tuple[int, int] = (0, 0)
+        if as_user:
+            uinfo = get_user_info(which_user)
+
+        env = os.environ.copy()
+        user_env = env.copy()
+        user_env["HOME"] = os.path.expanduser(f"~{which_user}")
+
+        proc = subprocess.run(
+            conf.commands.remove_flatpak(packages, as_user),
+            check=True,
+            user=uinfo[0],
+            group=uinfo[1],
+            env=user_env if as_user else env,
+        )
+
+        if not proc.returncode == 0:
+            raise err.UserFacingError(
+                f"Failed to remove flatpak packages. Process exited with code {proc.returncode}."
+            )
+
+        proc = subprocess.run(
+            conf.commands.remove_unused_flatpak(as_user),
+            check=True,
+            user=uinfo[0] if as_user else 0,
+            group=uinfo[1] if as_user else 0,
+            env=user_env if as_user else env,
+        )
+
+        if not proc.returncode == 0:
+            raise err.UserFacingError(
+                f"Failed to remove unused flatpak packages. Process exited with code {proc.returncode}."
+            )
 
 
 class Systemd:
@@ -946,12 +1149,15 @@ class Systemd:
             return
 
         try:
-            subprocess.run(conf.commands.enable_units(units),
+            subprocess.run(
-                           check=True,
+                conf.commands.enable_units(units),
-                           capture_output=conf.suppress_command_output)
+                check=True,
+                capture_output=conf.suppress_command_output,
+            )
         except subprocess.CalledProcessError as error:
             raise err.UserFacingError(
-                f"Failed to enable systemd units: {units}") from error
+                f"Failed to enable systemd units: {units}"
+            ) from error
         self.state.enabled_systemd_units += units
 
     def disable_units(self, units: list[str]):
@@ -962,12 +1168,15 @@ class Systemd:
             return
 
         try:
-            subprocess.run(conf.commands.disable_units(units),
+            subprocess.run(
-                           check=True,
+                conf.commands.disable_units(units),
-                           capture_output=conf.suppress_command_output)
+                check=True,
+                capture_output=conf.suppress_command_output,
+            )
         except subprocess.CalledProcessError as error:
             raise err.UserFacingError(
-                f"Failed to disable systemd units: {units}") from error
+                f"Failed to disable systemd units: {units}"
+            ) from error
         for unit in units:
             try:
                 self.state.enabled_systemd_units.remove(unit)
@@ -982,9 +1191,11 @@ class Systemd:
             return
 
         try:
-            subprocess.run(conf.commands.enable_user_units(units, user),
+            subprocess.run(
-                           check=True,
+                conf.commands.enable_user_units(units, user),
-                           capture_output=conf.suppress_command_output)
+                check=True,
+                capture_output=conf.suppress_command_output,
+            )
         except subprocess.CalledProcessError as error:
             raise err.UserFacingError(
                 f"Failed to enable systemd units: {units} for {user}."
@@ -1001,9 +1212,11 @@ class Systemd:
             return
 
         try:
-            subprocess.run(conf.commands.disable_user_units(units, user),
+            subprocess.run(
-                           check=True,
+                conf.commands.disable_user_units(units, user),
-                           capture_output=conf.suppress_command_output)
+                check=True,
+                capture_output=conf.suppress_command_output,
+            )
         except subprocess.CalledProcessError as error:
             raise err.UserFacingError(
                 f"Failed to disable systemd units: {units} for {user}."

src/decman/lib/fpm.py

@@ -11,18 +11,18 @@ Terminology:
 - all dependencies: normal dependencies and build dependencies combined
 """
 
-import shutil
-import subprocess
 import os
 import re
+import shutil
+import subprocess
 import typing
 
 import requests
 
 import decman
 import decman.config as conf
-import decman.lib as l
 import decman.error as err
+import decman.lib as l
 
 
 def strip_dependency(dep: str) -> str:
@@ -58,10 +58,18 @@ class PackageInfo:
     In case of AUR packages, these are fetched from AUR RPC.
     """
 
-    def __init__(self, pkgname: str, pkgbase: str, version: str,
+    def __init__(
-                 provides: list[str], dependencies: list[str],
+        self,
-                 make_dependencies: list[str], check_dependencies: list[str],
+        pkgname: str,
-                 git_url: str, pacman: l.Pacman):
+        pkgbase: str,
+        version: str,
+        provides: list[str],
+        dependencies: list[str],
+        make_dependencies: list[str],
+        check_dependencies: list[str],
+        git_url: str,
+        pacman: l.Pacman,
+    ):
         self.pkgname = pkgname
         self.pkgbase = pkgbase
         self.version = version
@@ -79,22 +87,23 @@ class PackageInfo:
             if pacman.is_installable(dep):
                 self.pacman_dependencies.append(dep)
             else:
-                self.foreign_dependencies_stripped.append(
+                self.foreign_dependencies_stripped.append(strip_dependency(dep))
-                    strip_dependency(dep))
 
         for make_dep in make_dependencies:
             if pacman.is_installable(make_dep):
                 self.pacman_make_dependencies.append(make_dep)
             else:
                 self.foreign_make_dependencies_stripped.append(
-                    strip_dependency(make_dep))
+                    strip_dependency(make_dep)
+                )
 
         for check_dep in check_dependencies:
             if pacman.is_installable(check_dep):
                 self.pacman_check_dependencies.append(check_dep)
             else:
                 self.foreign_check_dependencies_stripped.append(
-                    strip_dependency(check_dep))
+                    strip_dependency(check_dep)
+                )
 
     def pkg_file_prefix(self) -> str:
         """
@@ -103,8 +112,9 @@ class PackageInfo:
         return f"{self.pkgname}-{self.version}"
 
     @staticmethod
-    def from_user_package(user_package: decman.UserPackage,
+    def from_user_package(
-                          pacman: l.Pacman) -> "PackageInfo":
+        user_package: decman.UserPackage, pacman: l.Pacman
+    ) -> "PackageInfo":
         """
         Converts a UserPackage to PackageInfo
         """
@@ -132,8 +142,11 @@ class ForeignPackage:
 
     def __eq__(self, value: object, /) -> bool:
         if isinstance(value, self.__class__):
-            return self.name == value.name \
+            return (
-                   and self._all_recursive_foreign_deps == value._all_recursive_foreign_deps
+                self.name == value.name
+                and self._all_recursive_foreign_deps
+                == value._all_recursive_foreign_deps
+            )
         return False
 
     def __hash__(self) -> int:
@@ -145,8 +158,7 @@ class ForeignPackage:
     def __str__(self) -> str:
         return f"{self.name}"
 
-    def add_foreign_dependency_packages(self,
+    def add_foreign_dependency_packages(self, package_names: typing.Iterable[str]):
-                                        package_names: typing.Iterable[str]):
         """
         Adds dependencies to the package.
         """
@@ -174,8 +186,7 @@ class DepNode:
         Returns True if the given package name is in the parents of this DepNode.
         """
         for name, parent in self.parents.items():
-            if name == pkgname or parent.is_pkgname_in_parents_recursive(
+            if name == pkgname or parent.is_pkgname_in_parents_recursive(pkgname):
-                    pkgname):
                 return True
         return False
 
@@ -189,15 +200,15 @@ class DepGraph:
         self.package_nodes: dict[str, DepNode] = {}
         self._childless_node_names = set()
 
-    def add_requirement(self, child_pkgname: str,
+    def add_requirement(self, child_pkgname: str, parent_pkgname: typing.Optional[str]):
-                        parent_pkgname: typing.Optional[str]):
         """
         Adds a connection between two packages, creating the child package if it doesn't exist.
 
         The parent is the package that requires the child package.
         """
         child_node = self.package_nodes.get(
-            child_pkgname, DepNode(ForeignPackage(child_pkgname)))
+            child_pkgname, DepNode(ForeignPackage(child_pkgname))
+        )
         self.package_nodes[child_pkgname] = child_node
 
         if len(child_node.children) == 0:
@@ -212,7 +223,8 @@ class DepGraph:
             raise err.UserFacingError(
                 f"Foreign package dependency cycle detected involving '{child_pkgname}' \
 and '{parent_pkgname}'. Foreign package dependencies are also required \
-during package building and therefore dependency cycles cannot be handled.")
+during package building and therefore dependency cycles cannot be handled."
+            )
 
         parent_node.children[child_pkgname] = child_node
         child_node.parents[parent_pkgname] = parent_node
@@ -230,8 +242,7 @@ during package building and therefore dependency cycles cannot be handled.")
             childless_node = self.package_nodes[childless_node_name]
 
             for parent in childless_node.parents.values():
-                new_deps = childless_node.pkg.get_all_recursive_foreign_dep_pkgs(
+                new_deps = childless_node.pkg.get_all_recursive_foreign_dep_pkgs()
-                )
                 new_deps.add(childless_node.pkg.name)
                 parent.pkg.add_foreign_dependency_packages(new_deps)
                 del parent.children[childless_node_name]
@@ -254,6 +265,7 @@ class ExtendedPackageSearch:
         self._pacman = pacman
         self._package_info_cache: dict[str, PackageInfo] = {}
         self._dep_provider_cache: dict[str, PackageInfo] = {}
+        self._known_providers_cache: dict[str, list[str]] = {}
         self._user_packages: list[PackageInfo] = []
 
     def add_user_pkg(self, user_pkg: PackageInfo):
@@ -261,6 +273,15 @@ class ExtendedPackageSearch:
         Adds the given package to user packages.
         """
         self._user_packages.append(user_pkg)
+        self._cache_pkg(user_pkg)
+
+    def _cache_pkg(self, pkg: PackageInfo):
+        for provided_pkg in pkg.provides:
+            self._known_providers_cache[provided_pkg] = self._known_providers_cache.get(
+                provided_pkg, []
+            )
+            self._known_providers_cache[provided_pkg].append(pkg.pkgname)
+        self._package_info_cache[pkg.pkgname] = pkg
 
     def try_caching_packages(self, packages: list[str]):
         """
@@ -270,8 +291,7 @@ class ExtendedPackageSearch:
         times, because then those methods don't have to make new AUR RPC requests.
         """
 
-        packages = list(
+        packages = list(filter(lambda p: p not in self._package_info_cache, packages))
-            filter(lambda p: p not in self._package_info_cache, packages))
 
         if len(packages) == 0:
             return
@@ -281,8 +301,7 @@ class ExtendedPackageSearch:
         max_pkgs_per_request = 200
 
         while packages:
-            to_request = map(lambda p: f"arg[]={p}",
+            to_request = map(lambda p: f"arg[]={p}", packages[:max_pkgs_per_request])
-                             packages[:max_pkgs_per_request])
             packages = packages[max_pkgs_per_request:]
 
             url = f"https://aur.archlinux.org/rpc/v5/info?{'&'.join(to_request)}"
@@ -293,8 +312,7 @@ class ExtendedPackageSearch:
                 d = request.json()
 
                 if d["type"] == "error":
-                    raise err.UserFacingError(
+                    raise err.UserFacingError(f"AUR RPC returned error: {d['error']}")
-                        f"AUR RPC returned error: {d['error']}")
 
                 for result in d["results"]:
                     pkgname = result["Name"]
@@ -304,9 +322,8 @@ class ExtendedPackageSearch:
 
                     for user_package in self._user_packages:
                         if user_package.pkgname == pkgname:
-                            l.print_debug(
+                            l.print_debug(f"'{pkgname}' found in user packages.")
-                                f"'{pkgname}' found in user packages.")
+                            self._cache_pkg(user_package)
-                            self._package_info_cache[pkgname] = user_package
                             break
                     else:  # if not in user_packages then:
                         info = PackageInfo(
@@ -317,10 +334,10 @@ class ExtendedPackageSearch:
                             make_dependencies=result.get("MakeDepends", []),
                             check_dependencies=result.get("CheckDepends", []),
                             provides=result.get("Provides", []),
-                            git_url=
+                            git_url=f"https://aur.archlinux.org/{result['PackageBase']}.git",
-                            f"https://aur.archlinux.org/{result['PackageBase']}.git",
+                            pacman=self._pacman,
-                            pacman=self._pacman)
+                        )
-                        self._package_info_cache[pkgname] = info
+                        self._cache_pkg(info)
 
                 l.print_debug("Request completed.")
             except (requests.RequestException, KeyError) as e:
@@ -345,7 +362,7 @@ class ExtendedPackageSearch:
         for user_package in self._user_packages:
             if user_package.pkgname == package:
                 l.print_debug(f"'{package}' found in user packages.")
-                self._package_info_cache[package] = user_package
+                self._cache_pkg(user_package)
                 return user_package
 
         url = f"https://aur.archlinux.org/rpc/v5/info/{package}"
@@ -355,8 +372,7 @@ class ExtendedPackageSearch:
             d = request.json()
 
             if d["type"] == "error":
-                raise err.UserFacingError(
+                raise err.UserFacingError(f"AUR RPC returned error: {d['error']}")
-                    f"AUR RPC returned error: {d['error']}")
 
             if d["resultcount"] == 0:
                 l.print_debug(f"'{package}' not found.")
@@ -373,11 +389,11 @@ class ExtendedPackageSearch:
                 make_dependencies=result.get("MakeDepends", []),
                 check_dependencies=result.get("CheckDepends", []),
                 provides=result.get("Provides", []),
-                git_url=
+                git_url=f"https://aur.archlinux.org/{result['PackageBase']}.git",
-                f"https://aur.archlinux.org/{result['PackageBase']}.git",
+                pacman=self._pacman,
-                pacman=self._pacman)
+            )
 
-            self._package_info_cache[package] = info
+            self._cache_pkg(info)
 
             return info
         except (requests.RequestException, KeyError) as e:
@@ -386,8 +402,7 @@ class ExtendedPackageSearch:
                 f"Failed to fetch package information for {package} from AUR RPC."
             ) from e
 
-    def find_provider(
+    def find_provider(self, stripped_dependency: str) -> typing.Optional[PackageInfo]:
-            self, stripped_dependency: str) -> typing.Optional[PackageInfo]:
         """
         Finds a provider for a dependency.
 
@@ -410,25 +425,31 @@ class ExtendedPackageSearch:
 
         l.print_debug("No exact name matches found. Finding providers.")
 
-        user_pkg_results = []
+        known_pkg_results = self._known_providers_cache.get(stripped_dependency, [])
         for user_package in self._user_packages:
-            if stripped_dependency in user_package.provides:
+            if (
-                user_pkg_results.append(user_package.pkgname)
+                stripped_dependency in user_package.provides
+                and stripped_dependency not in known_pkg_results
+            ):
+                known_pkg_results.append(user_package.pkgname)
 
-        if len(user_pkg_results) == 1:
+        if len(known_pkg_results) == 1:
-            pkg = self.get_package_info(user_pkg_results[0])
+            pkg = self.get_package_info(known_pkg_results[0])
             assert pkg is not None
             l.print_debug(
-                f"Single provider for '{stripped_dependency}' found in user packages: '{pkg}'."
+                f"Single provider for '{stripped_dependency}' found in known packages: '{pkg}'."
             )
             self._dep_provider_cache[stripped_dependency] = pkg
             return pkg
 
-        if len(user_pkg_results) > 1:
+        if len(known_pkg_results) > 1:
-            return self._choose_provider(stripped_dependency, user_pkg_results,
+            return self._choose_provider(
-                                         "user packages")
+                stripped_dependency, known_pkg_results, "user packages"
+            )
 
-        url = f"https://aur.archlinux.org/rpc/v5/search/{stripped_dependency}?by=provides"
+        url = (
+            f"https://aur.archlinux.org/rpc/v5/search/{stripped_dependency}?by=provides"
+        )
         l.print_debug(
             f"Requesting providers for '{stripped_dependency}' from AUR. URL = {url}"
         )
@@ -437,8 +458,7 @@ class ExtendedPackageSearch:
             d = request.json()
 
             if d["type"] == "error":
-                raise err.UserFacingError(
+                raise err.UserFacingError(f"AUR RPC returned error: {d['error']}")
-                    f"AUR RPC returned error: {d['error']}")
 
             if d["resultcount"] == 0:
                 l.print_debug(f"'{stripped_dependency}' not found.")
@@ -461,8 +481,9 @@ class ExtendedPackageSearch:
                 f"Failed to search for {stripped_dependency} from AUR RPC."
             ) from e
 
-    def _choose_provider(self, dep: str, possible_providers: list[str],
+    def _choose_provider(
-                         where: str) -> typing.Optional[PackageInfo]:
+        self, dep: str, possible_providers: list[str], where: str
+    ) -> typing.Optional[PackageInfo]:
         min_selection = 1
         max_selection = len(possible_providers)
         l.print_summary(
@@ -478,7 +499,8 @@ class ExtendedPackageSearch:
             f"Select a provider [{min_selection}-{max_selection}] (default: {min_selection}): ",
             min_selection,
             max_selection,
-            default=min_selection)
+            default=min_selection,
+        )
 
         info = self.get_package_info(possible_providers[selection - 1])
         if info is not None:
@@ -541,16 +563,17 @@ class ForeignPackageManager:
     Class for dealing with foreign packages.
     """
 
-    def __init__(self, store: l.Store, pacman: l.Pacman,
+    def __init__(self, store: l.Store, pacman: l.Pacman, search: ExtendedPackageSearch):
-                 search: ExtendedPackageSearch):
         self._store = store
         self._pacman = pacman
         self._search = search
 
-    def upgrade(self,
+    def upgrade(
-                upgrade_devel: bool = False,
+        self,
-                force: bool = False,
+        upgrade_devel: bool = False,
-                ignored_pkgs: typing.Optional[set[str]] = None):
+        force: bool = False,
+        ignored_pkgs: typing.Optional[set[str]] = None,
+    ):
         """
         Upgrades all foreign packages.
         """
@@ -561,11 +584,9 @@ class ForeignPackageManager:
 
         all_foreign_pkgs = self._pacman.get_versioned_foreign_packages()
         all_explicit_pkgs = set(self._pacman.get_installed())
-        l.print_debug(
+        l.print_debug(f"Foreign packages to check for upgrades: {all_foreign_pkgs}")
-            f"Foreign packages to check for upgrades: {all_foreign_pkgs}")
 
-        self._search.try_caching_packages(
+        self._search.try_caching_packages(list(map(lambda p: p[0], all_foreign_pkgs)))
-            list(map(lambda p: p[0], all_foreign_pkgs)))
 
         as_explicit = []
         as_deps = []
@@ -579,8 +600,7 @@ class ForeignPackageManager:
                     f"Failed to find '{pkg}' from AUR or user provided packages."
                 )
 
-            if self.should_upgrade_package(pkg, ver, info.version,
+            if self.should_upgrade_package(pkg, ver, info.version, upgrade_devel):
-                                           upgrade_devel):
                 if pkg in all_explicit_pkgs:
                     as_explicit.append(pkg)
                 else:
@@ -592,10 +612,12 @@ class ForeignPackageManager:
 
         self.install(as_explicit, as_deps, force)
 
-    def install(self,
+    def install(
-                foreign_pkgs: list[str],
+        self,
-                foreign_dep_pkgs: typing.Optional[list[str]] = None,
+        foreign_pkgs: list[str],
-                force: bool = False):
+        foreign_dep_pkgs: typing.Optional[list[str]] = None,
+        force: bool = False,
+    ):
         """
         Installs the given foreign packages and their dependencies (both pacman/AUR).
         """
@@ -607,39 +629,44 @@ class ForeignPackageManager:
             return
 
         resolved_dependencies = self.resolve_dependencies(
-            foreign_pkgs, foreign_dep_pkgs)
+            foreign_pkgs, foreign_dep_pkgs
+        )
 
         l.print_list(
             "The following foreign packages will be installed explicitly:",
             list(resolved_dependencies.foreign_pkgs),
-            level=l.SUMMARY)
+            level=l.SUMMARY,
+        )
 
         l.print_list(
             "The following foreign packages will be installed as dependencies:",
             list(resolved_dependencies.foreign_dep_pkgs),
-            level=l.SUMMARY)
+            level=l.SUMMARY,
+        )
 
         l.print_list(
             "The following foreign packages will be built in order to install other packages. They will not be installed:",
             list(resolved_dependencies.foreign_build_dep_pkgs),
-            level=l.SUMMARY)
+            level=l.SUMMARY,
+        )
 
         if not l.prompt_confirm("Proceed?", default=True):
             raise err.UserFacingError("Installing aborted.")
 
         l.print_summary("Installing foreign package dependencies from pacman.")
-        self._pacman.install_dependencies(
+        self._pacman.install_dependencies(list(resolved_dependencies.pacman_deps))
-            list(resolved_dependencies.pacman_deps))
 
         try:
-            with PackageBuilder(self._search, self._store,
+            with PackageBuilder(
-                                resolved_dependencies) as builder:
+                self._search, self._store, resolved_dependencies
+            ) as builder:
                 while resolved_dependencies.build_order:
                     to_build = resolved_dependencies.build_order.pop(0)
 
                     pkgbase = resolved_dependencies.get_pkgbase(to_build)
                     package_names = resolved_dependencies.get_pkgs_with_common_pkgbase(
-                        to_build)
+                        to_build
+                    )
 
                     packages = [
                         resolved_dependencies.packages[pkgname]
@@ -663,16 +690,17 @@ class ForeignPackageManager:
 
         if package_files_to_install or force:
             l.print_summary("Installing foreign packages.")
-            self._pacman.install_files(package_files_to_install,
+            self._pacman.install_files(
-                                       as_explicit=list(
+                package_files_to_install,
-                                           resolved_dependencies.foreign_pkgs))
+                as_explicit=list(resolved_dependencies.foreign_pkgs),
+            )
         else:
             l.print_summary("No packages to install.")
 
     def resolve_dependencies(
         self,
         foreign_pkgs: list[str],
-        foreign_dep_pkgs: typing.Optional[list[str]] = None
+        foreign_dep_pkgs: typing.Optional[list[str]] = None,
     ) -> ResolvedDependencies:
         """
         Resolves foreign dependencies of foreign packages.
@@ -690,7 +718,7 @@ class ForeignPackageManager:
 
         graph = DepGraph()
 
-        for name in (foreign_pkgs + foreign_dep_pkgs):
+        for name in foreign_pkgs + foreign_dep_pkgs:
             graph.add_requirement(name, None)
 
         seen_packages = set(foreign_pkgs + foreign_dep_pkgs)
@@ -709,8 +737,7 @@ class ForeignPackageManager:
 
             add_to.add(dep_info.pkgname)
 
-            l.print_debug(
+            l.print_debug(f"Adding dependency {dep_info.pkgname} to package {pkgname}.")
-                f"Adding dependency {dep_info.pkgname} to package {pkgname}.")
             graph.add_requirement(dep_info.pkgname, pkgname)
             if dep_info.pkgname not in seen_packages:
                 to_process.append(dep_info.pkgname)
@@ -728,10 +755,14 @@ class ForeignPackageManager:
             result.pacman_deps.update(info.pacman_dependencies)
             result.add_pkgbase_info(pkgname, info.pkgbase)
 
-            build_deps = info.foreign_make_dependencies_stripped + info.foreign_check_dependencies_stripped
+            build_deps = (
+                info.foreign_make_dependencies_stripped
+                + info.foreign_check_dependencies_stripped
+            )
 
             self._search.try_caching_packages(
-                info.foreign_dependencies_stripped + build_deps)
+                info.foreign_dependencies_stripped + build_deps
+            )
 
             for depname in info.foreign_dependencies_stripped:
                 process_dep(pkgname, depname, result.foreign_dep_pkgs)
@@ -758,26 +789,29 @@ class ForeignPackageManager:
 
         return result
 
-    def should_upgrade_package(self,
+    def should_upgrade_package(
-                               package: str,
+        self,
-                               installed_version: str,
+        package: str,
-                               fetched_version: str,
+        installed_version: str,
-                               upgrade_devel=False) -> bool:
+        fetched_version: str,
+        upgrade_devel=False,
+    ) -> bool:
         """
         Returns True if a package should be upgraded.
         """
 
         if upgrade_devel and is_devel(package):
-            l.print_debug(
+            l.print_debug(f"Package {package} is devel package. It should be upgraded.")
-                f"Package {package} is devel package. It should be upgraded.")
             return True
 
         try:
             result = int(
-                subprocess.run(conf.commands.compare_versions(
+                subprocess.run(
-                    installed_version, fetched_version),
+                    conf.commands.compare_versions(installed_version, fetched_version),
-                               check=True,
+                    check=True,
-                               stdout=subprocess.PIPE).stdout.decode())
+                    stdout=subprocess.PIPE,
+                ).stdout.decode()
+            )
             should_upgrade = result < 0
             l.print_debug(
                 f"Installed version is: {installed_version}. Available version is {fetched_version}. Should upgrade: {should_upgrade}"
@@ -786,7 +820,8 @@ class ForeignPackageManager:
         except (ValueError, subprocess.CalledProcessError) as error:
             l.print_error(f"{error}")
             raise err.UserFacingError(
-                "Failed to compare versions using vercmp.") from error
+                "Failed to compare versions using vercmp."
+            ) from error
 
 
 class PackageBuilder:
@@ -796,8 +831,12 @@ class PackageBuilder:
 
     always_included_packages = ["base-devel", "git"]
 
-    def __init__(self, search: ExtendedPackageSearch, store: l.Store,
+    def __init__(
-                 resolved_deps: ResolvedDependencies):
+        self,
+        search: ExtendedPackageSearch,
+        store: l.Store,
+        resolved_deps: ResolvedDependencies,
+    ):
         self._search = search
         self._store = store
         self._resolved_deps = resolved_deps
@@ -850,7 +889,8 @@ class PackageBuilder:
             os.chdir(pkgbuild_dir)
 
             git_url_info = self._search.get_package_info(
-                self._resolved_deps.get_some_pkgname(pkgbase))
+                self._resolved_deps.get_some_pkgname(pkgbase)
+            )
 
             # Because all dependencies and packages should be resolved during the creation
             # of ResolvedDependencies. git_url should not be None.
@@ -869,16 +909,16 @@ class PackageBuilder:
         mkarchroot_env_vars = os.environ.copy()
         try:
             del mkarchroot_env_vars["GNUPGHOME"]
-            l.print_debug(
+            l.print_debug("Removed GNUPGHOME variable from mkarchroot environment.")
-                "Removed GNUPGHOME variable from mkarchroot environment.")
         except KeyError:
             pass
 
-        subprocess.run(conf.commands.make_chroot(self.chroot_dir,
+        subprocess.run(
-                                                 list(self._pkgs_in_chroot)),
+            conf.commands.make_chroot(self.chroot_dir, list(self._pkgs_in_chroot)),
-                       env=mkarchroot_env_vars,
+            env=mkarchroot_env_vars,
-                       check=True,
+            check=True,
-                       capture_output=conf.suppress_command_output)
+            capture_output=conf.suppress_command_output,
+        )
 
     def remove_build_environment(self):
         """
@@ -886,8 +926,9 @@ class PackageBuilder:
         """
         shutil.rmtree(conf.build_dir)
 
-    def build_packages(self, package_base: str, packages: list[ForeignPackage],
+    def build_packages(
-                       force: bool):
+        self, package_base: str, packages: list[ForeignPackage], force: bool
+    ):
         """
         Builds package(s) with the same package base.
 
@@ -906,8 +947,7 @@ class PackageBuilder:
 
         l.print_info(f"Building '{' '.join(package_names)}'.")
 
-        chroot_new_pacman_pkgs, chroot_pkg_files = self._get_chroot_packages(
+        chroot_new_pacman_pkgs, chroot_pkg_files = self._get_chroot_packages(packages)
-            packages)
 
         pkgbuild_dir = self.pkgbase_dir_map[package_base]
         os.chdir(pkgbuild_dir)
@@ -918,19 +958,24 @@ class PackageBuilder:
 
         l.print_info("Installing build dependencies to chroot.")
 
-        subprocess.run(conf.commands.install_chroot_packages(
+        subprocess.run(
-            self.chroot_dir,
+            conf.commands.install_chroot_packages(
-            chroot_new_pacman_pkgs + PackageBuilder.always_included_packages),
+                self.chroot_dir,
-                       check=True,
+                chroot_new_pacman_pkgs + PackageBuilder.always_included_packages,
-                       capture_output=conf.suppress_command_output)
+            ),
+            check=True,
+            capture_output=conf.suppress_command_output,
+        )
 
         l.print_info("Making package.")
 
-        subprocess.run(conf.commands.make_chroot_pkg(self.chroot_wd_dir,
+        subprocess.run(
-                                                     conf.makepkg_user,
+            conf.commands.make_chroot_pkg(
-                                                     chroot_pkg_files),
+                self.chroot_wd_dir, conf.makepkg_user, chroot_pkg_files
-                       check=True,
+            ),
-                       capture_output=conf.quiet_output)
+            check=True,
+            capture_output=conf.quiet_output,
+        )
 
         for pkgname in package_names:
             file = self._find_pkgfile(pkgname, pkgbuild_dir)
@@ -952,16 +997,25 @@ class PackageBuilder:
 
         l.print_info("Removing build dependencies from chroot.")
 
-        # FIX: If installed packages are virtual packages, removing them wont succeed.
         if len(chroot_new_pacman_pkgs) != 0:
             to_remove = []
             for p in chroot_new_pacman_pkgs:
                 if p not in self._pkgs_in_chroot:
-                    to_remove.append(strip_dependency(p))
+                    real_pkgname = (
-            subprocess.run(conf.commands.remove_chroot_packages(
+                        subprocess.run(
-                self.chroot_dir, to_remove),
+                            conf.commands.resolve_real_name(self.chroot_dir, p),
-                           check=True,
+                            check=True,
-                           capture_output=conf.suppress_command_output)
+                            stdout=subprocess.PIPE,
+                        )
+                        .stdout.decode()
+                        .strip()
+                    )
+                    to_remove.append(real_pkgname)
+            subprocess.run(
+                conf.commands.remove_chroot_packages(self.chroot_dir, to_remove),
+                check=True,
+                capture_output=conf.suppress_command_output,
+            )
 
         l.print_info(f"Finished building: '{' '.join(package_names)}'.")
 
@@ -984,7 +1038,7 @@ class PackageBuilder:
         return True
 
     def _get_chroot_packages(
-            self, pkgs_to_build: list[ForeignPackage]
+        self, pkgs_to_build: list[ForeignPackage]
     ) -> tuple[list[str], list[str]]:
         """
         Returns a tuple of pacman build dependencies and built foreign pkgs files that are needed
@@ -1030,8 +1084,10 @@ class PackageBuilder:
 
         for foreign_pkg in chroot_foreign_pkgs:
             entry = self._store.get_package(foreign_pkg)
-            assert entry is not None, "Build order determines that the dependencies are built \
+            assert entry is not None, (
+                "Build order determines that the dependencies are built \
 before and thus are found in the cache."
+            )
 
             _, file = entry
 
@@ -1070,32 +1126,55 @@ before and thus are found in the cache."
         The user is prompted to review the PKGBUILD and confirm if the package should be built.
         """
         try:
-            subprocess.run(conf.commands.git_clone(git_url, "."),
+            subprocess.run(
-                           check=True,
+                conf.commands.git_clone(git_url, "."),
-                           capture_output=conf.suppress_command_output)
+                check=True,
+                capture_output=conf.suppress_command_output,
+            )
 
-            if l.prompt_confirm(f"Review PKGBUILD or show diff for {pkgbase}?",
+            if l.prompt_confirm(
-                                default=True):
+                f"Review PKGBUILD or show diff for {pkgbase}?", default=True
-                latest_reviewed_commit = self._store.pkgbuild_latest_reviewed_commits.get(
+            ):
-                    pkgbase)
+                latest_reviewed_commit = (
-                if latest_reviewed_commit is None:
+                    self._store.pkgbuild_latest_reviewed_commits.get(pkgbase)
+                )
+
+                git_commit_ids = (
+                    subprocess.run(
+                        conf.commands.git_log_commit_ids(),
+                        check=True,
+                        stdout=subprocess.PIPE,
+                    )
+                    .stdout.decode()
+                    .strip()
+                    .split("\n")
+                )
+
+                if (
+                    latest_reviewed_commit is None
+                    or latest_reviewed_commit not in git_commit_ids
+                ):
                     for file in os.scandir("."):
                         if file.is_file() and not file.name.startswith("."):
-                            subprocess.run(conf.commands.review_file(
+                            subprocess.run(
-                                file.path),
+                                conf.commands.review_file(file.path), check=True
-                                           check=True)
+                            )
                 else:
                     subprocess.run(
-                        conf.commands.git_diff(latest_reviewed_commit),
+                        conf.commands.git_diff(latest_reviewed_commit), check=True
-                        check=True)
+                    )
 
             if l.prompt_confirm("Build this package?", default=True):
-                commit_id = subprocess.run(
+                commit_id = (
-                    conf.commands.git_get_commit_id(),
+                    subprocess.run(
-                    check=True,
+                        conf.commands.git_get_commit_id(),
-                    capture_output=True).stdout.decode().strip()
+                        check=True,
-                self._store.pkgbuild_latest_reviewed_commits[
+                        capture_output=True,
-                    pkgbase] = commit_id
+                    )
+                    .stdout.decode()
+                    .strip()
+                )
+                self._store.pkgbuild_latest_reviewed_commits[pkgbase] = commit_id
             else:
                 raise err.UserFacingError("Building aborted.")
 

tests/test_source_resolution.py

@@ -1,12 +1,13 @@
 # pylint: disable=missing-module-docstring,missing-class-docstring,missing-function-docstring
 
+from typing import override
 import unittest
+
+from decman import Module, UserPackage
 from decman.lib import Source, Store
-from decman import UserPackage, Module
 
 
 class ExistingTestModule(Module):
-
     def __init__(self):
         self.on_enable_executed = False
         self.on_disable_executed = False
@@ -28,7 +29,6 @@ class ExistingTestModule(Module):
 
 
 class ExistingChangedVersionTestModule(Module):
-
     def __init__(self):
         self.on_enable_executed = False
         self.on_disable_executed = False
@@ -50,7 +50,6 @@ class ExistingChangedVersionTestModule(Module):
 
 
 class EnabledTestModule(Module):
-
     def __init__(self):
         self.on_enable_executed = False
         self.on_disable_executed = False
@@ -76,9 +75,11 @@ class EnabledTestModule(Module):
     def systemd_user_units(self) -> dict[str, list[str]]:
         return {"muser": ["M_u1.service"]}
 
+    def flatpak_packages(self) -> list[str]:
+        return ["M_f1", "M_f2"]
+
 
 class DisabledTestModule(Module):
-
     def __init__(self):
         self.on_enable_executed = False
         self.on_disable_executed = False
@@ -106,7 +107,6 @@ class DisabledTestModule(Module):
 
 
 class TestSource(unittest.TestCase):
-
     def setUp(self):
         self.disabled_module = DisabledTestModule()
         self.enabled_module = EnabledTestModule()
@@ -133,7 +133,7 @@ class TestSource(unittest.TestCase):
                     version="1",
                     dependencies=["d2"],
                     git_url="/am/url/yes",
-                )
+                ),
             },
             ignored_packages={"i1", "i2"},
             systemd_units={"1.service", "2.timer"},
@@ -141,11 +141,13 @@ class TestSource(unittest.TestCase):
             modules=modules,
             files={},
             directories={},
+            flatpak_packages={"f1", "f2", "f3"},
+            flatpak_user_packages={"fu1", "fu2", "fu3"},
+            ignored_flatpak_packages={"i1", "i2"},
         )
 
         store = Store()
-        store.enabled_systemd_units.extend(
+        store.enabled_systemd_units.extend(["1.service", "3.service", "M_1.service"])
-            ["1.service", "3.service", "M_1.service"])
         store.add_enabled_user_systemd_unit("user", "u1.service")
         store.add_enabled_user_systemd_unit("user", "u3.service")
         store.enabled_modules = {
@@ -174,16 +176,19 @@ class TestSource(unittest.TestCase):
         self.currently_installed_packages = currently_installed_packages
 
     def test_all_enabled_modules(self):
-        enabled_modules = [("Enabled", "1"), ("Existing", "1"),
+        enabled_modules = [
-                           ("ExistingChanged", "2")]
+            ("Enabled", "1"),
-        self.assertCountEqual(self.source.all_enabled_modules(),
+            ("Existing", "1"),
-                              enabled_modules)
+            ("ExistingChanged", "2"),
+        ]
+        self.assertCountEqual(self.source.all_enabled_modules(), enabled_modules)
 
     def test_files_to_remove(self):
         created_files = ["/test/file1", "/test/file4"]
         self.assertCountEqual(
             self.source.files_to_remove(self.store, created_files),
-            ["/test/file2", "/test/file3"])
+            ["/test/file2", "/test/file3"],
+        )
 
     def test_after_update_executed(self):
         self.source.run_after_update()
@@ -197,8 +202,7 @@ class TestSource(unittest.TestCase):
         self.source.run_after_version_change(self.store)
 
         self.assertTrue(self.enabled_module.after_version_change_executed)
-        self.assertTrue(
+        self.assertTrue(self.existing_module_changed.after_version_change_executed)
-            self.existing_module_changed.after_version_change_executed)
         self.assertFalse(self.existing_module.after_version_change_executed)
         self.assertFalse(self.disabled_module.after_version_change_executed)
 
@@ -233,10 +237,7 @@ class TestSource(unittest.TestCase):
     def test_user_units_to_enable(self):
         self.assertDictEqual(
             self.source.user_units_to_enable(self.store),
-            {
+            {"user": ["u2.timer"], "muser": ["M_u1.service"]},
-                "user": ["u2.timer"],
-                "muser": ["M_u1.service"]
-            },
         )
 
     def test_user_units_to_disable(self):
@@ -247,15 +248,13 @@ class TestSource(unittest.TestCase):
 
     def test_pacman_packages_to_install(self):
         self.assertCountEqual(
-            self.source.pacman_packages_to_install(
+            self.source.pacman_packages_to_install(self.currently_installed_packages),
-                self.currently_installed_packages),
             ["p3", "M_p1", "M_p2"],
         )
 
     def test_foreign_packages_to_install(self):
         self.assertCountEqual(
-            self.source.foreign_packages_to_install(
+            self.source.foreign_packages_to_install(self.currently_installed_packages),
-                self.currently_installed_packages),
             ["A1", "U2"],
         )
 
@@ -264,3 +263,41 @@ class TestSource(unittest.TestCase):
             self.source.packages_to_remove(self.currently_installed_packages),
             ["p4", "A4", "M_A1", "M_A2"],
         )
+
+
+class TestModuleUserServices(unittest.TestCase):
+    class ModuleWithUserServiceOne(Module):
+        def __init__(self):
+            super().__init__("one", True, "0")
+
+        def systemd_user_units(self) -> dict[str, list[str]]:
+            return {"user": ["foo.service"]}
+
+    class ModuleWithUserServiceTwo(Module):
+        def __init__(self):
+            super().__init__("two", True, "0")
+
+        def systemd_user_units(self) -> dict[str, list[str]]:
+            return {"user": ["bar.service"]}
+
+    def setUp(self) -> None:
+        self.source = Source(
+            pacman_packages=set(),
+            aur_packages=set(),
+            user_packages=set(),
+            ignored_packages=set(),
+            systemd_units=set(),
+            systemd_user_units={},
+            files={},
+            directories={},
+            modules={self.ModuleWithUserServiceOne(), self.ModuleWithUserServiceTwo()},
+            flatpak_packages=set(),
+            flatpak_user_packages=set(),
+            ignored_flatpak_packages=set(),
+        )
+        self.store = Store()
+
+    def test_user_units_to_enable(self):
+        result = self.source.user_units_to_enable(self.store)
+        self.assertEqual(len(result), 1)
+        self.assertCountEqual(result["user"], ["foo.service", "bar.service"])